Pfal Network files
MetNetMaker representations can be viewed in any spreadsheet but advanced features can only be accessed using MetNetMaker*. All SBML and visualisation files are created within MetNetMaker by loading the .xls file and then exporting again using the appropriate button as shown below.
This site is not guaranteed to be up-to-date. New versions of each pathway may be available and linking reactions between each pathway may be required.
FINAL MODEL
| MetNetMaker .xls |
SBML L2V1 .xml with constraints |
Cytoscape Session .cys |
Cytoscape Session .cys with fluxes |
Annotated inkscape model .svg with fluxes |
Annotated model .png with fluxes |
|
| Model included in my thesis | here... | here... | here... | here... | here... |
here... |
1.1 Carbon Metabolism
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Glycolysis (00010) | here... | here... | here... | here... | here... |
| Mitochondrial TCA Cycle (00020) | here... | here... | Coming soon... | here... | here... |
| Pentose Phosphate Cycle (00030) | here... | here... | Coming soon... | here... | here... |
| Aminosugars Metabolism (cytosol) (00530) | here... | here... | Coming soon... | here... | here... |
| Pyruvate Metabolism (cytosol) (00620) | here... | here... | Coming soon... | here... | here... |
| Pyruvate Metabolism (mitochondrion)
(00620) |
here... | here... | Coming soon... | here... | here... |
| Pyruvate Metabolism (apicoplast) (00620) | here... | here... | Coming soon... | here... | here... |
| Combined Carbon Metabolism (1.1) | here... | here... | Coming soon... | here... | here... |
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
1.2 Energy Metabolism
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Nitrogen metabolism (00910) | here... | here... | Coming soon... | here... | here... |
_RID.svg){kind=link}
_EC.svg){kind=link}
1.3 Lipid Metabolism
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Fatty Acid Synthesis in the Apicoplast | here... | here... | Coming soon... | here... | here... |
| Inositol phosphate metabolism (00562) | here... | here... | Coming soon... | here... | here... |
| Utilization of phospholipids (00564) | here... | here... | Coming soon... | here... | here... |
| Spingomyelin and ceramide metabolism
(00600) |
here... | here... | Coming soon... | here... | here... |
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
1.4 Nucleotide Metabolism
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Purine metabolism (Top) (00230) | here... | here... | Coming soon... | here... | here... |
| Purine metabolism (Bottom) (00230) | here... | here... | Coming soon... | here... | here... |
| Pyrimidine metabolism (00240) | here... | here... | Coming soon... | here... | here... |
 (00230)_RID.svg){kind=link}
 (00230)_EC.svg){kind=link}
 (00230)_RID.svg){kind=link}
 (00230)_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
1.5 Amino Acid Metabolism
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Asparagine and Aspartate metabolism | here... | here... | Coming soon... | here... | here... |
| Selenocysteine biosynthesis | here... | here... | Coming soon... | here... | here... |
| Glutamate metabolism (00251) | here... | here... | Coming soon... | here... | here... |
| Glycine and Serine metabolism (00260) | here... | here... | Coming soon... | here... | here... |
| Leucine, Isoleucine and Valine metabolism
(00280 and 00290) |
here... | here... | Coming soon... | here... | here... |
| Lysine metabolism (00300 and 00310) | here... | here... | Coming soon... | here... | here... |
| Arginine and proline metabolism (00330) | here... | here... | Coming soon... | here... | here... |
| Phenylalanine and Tyrosine Metabolism
(00350 and 00360) |
here... | here... | Coming soon... | here... | here... |
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
1.7 Glycan Biosynthesis
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| Dolichol metabolism (N-glycan biosynthesis) (00510) | here... | here... | Coming soon... | here... | here... |
| GPI Anchor Biosynthesis (00563) | here... | here... | Coming soon... | here... | here... |
1.9 Metabolism of Cofactors and Vitamins
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| CoA biosynthesis (00770) (00510) | here... | here... | Coming soon... | here... | here... |
| Folate Biosynthesis (00790) | here... | here... | Coming soon... | here... | here... |
| Nicotinate and Nicotinamide Metabolism (00760) | here... | here... | Coming soon... | here... | here... |
| Porphyrin metabolism (00860) | here... | here... | Coming soon... | here... | here... |
| Shikimate pathway | here... | here... | Coming soon... | here... | here... |
| Thiamine metabolism (00730) | here... | here... | Coming soon... | here... | here... |
| Vitamin B6 metabolism (00750) | here... | here... | Coming soon... | here... | here... |
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
_RID.svg){kind=link}
_EC.svg){kind=link}
Useful Combinations
| Pathway (KEGG map number) | MetNetMaker .xls |
SBML L2V4 .xml |
Cytoscape Session .cys |
KEGG projection of ReactionIDs .svg |
KEGG projection of EC numbers .svg |
| 1.1 All Carbon Metabolism | here... | here... | here... | here... | here... |
| 1.3 All Lipid Metabolism | here... | here... | Coming soon... | here... | here... |
| 1.4 All Nucleotide Metabolism | here... | here... | here... | here... | here... |
| 1.5 All Amino Acid Metabolism | here... | here... | here... | here... | here... |
| 1.7 All Glycan biosynthesis | here... | here... | Coming soon... | here... | here... |
| 1.9 All Metabolism of Cofactors and Vitamins | here... | here... | Coming soon... | here... | here... |
| All Pathways | here... | here... | partial, here... | here... | here... |
*MetNetMaker 1.6 with advanced visualisation capabilities will be released shortly, please email me to get it now. Some of the networks may contain custom reactions that need to be loaded using the "Restore User Reactions" button on the MetNetMaker Ribbon and loading this file.