kegglogo  Pfal Network files

Tom Forth,

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.

MetNetMaker Export Options Toolbar

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...

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...

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...

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...

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...

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...

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.