A metabolic pathway consists of multiple processes connected together. A process is any reaction involving molecular entities, and has zero (i.e., a non-enzymatic process) or more catalyzing enzymes, one or more substrates and products, zero or more co-factor-ins, co-factor-outs, inhibitors, or activators.
The substrates of the process are indicated by the pink node(s) at the left; products are indicated using circular purple node(s) at the right. The yellow and orange circle shaped nodes on the top indicate cofactor-ins and cofactor-outs respectively. The light-blue node(s) on the bottom left hand side indicate inhibitors; the dark-blue node(s) on the bottom right hand side indicates activators of the process; and the blue node(s) indicates regulators. The catalyzing protein is indicated using a square shaped node at the center of the process.
Edges can be in many shapes depending on the type of the interaction; for example, arrow-edges means reaction from/to substrates or products, curve-edges are cofactors, T-shape edges represents inhibitor, etc.
All substrate and product nodes are generally visualized only once (green nodes) in the metabolic pathway graph. However, there are some common molecules (e.g. H2O, O2, etc.) which occur many times in the pathway. Drawing these molecules only once causes multiple cross-edges among processes, thus increasing the complexity of the graph. Therefore, these common molecules are allowed to be redundant in the metabolic pathway graph.
