Fig. 2

Examples for general reaction categories. This figure displays example reactions in SBGN for each of the twelve categories that are used to determine applicable rate equations. a) Reaction with a non-enzyme catalyst. The ion I1 catalyzes this association reaction, which can therefore not be considered enzyme catalyzed. In addition, this reaction is also modulated in a feedback inhibition loop, has an integer stoichiometry, and two reactants. b) Gene-regulatory processes. Reaction re2a assembles an mRNA molecule from a source of bases (transcription), enabled by the a specific gene. This mRNA in turn (re2b) enables the assembly of a protein from a source of amino acids (translation). In a feedback inhibition loop, the protein interferes with the transcription of its own gene. c) Uni-uni enzyme reaction. This schematic conforms the classical Michaelis-Menten mechanism. d) Bi-uni enzyme reaction. This association reaction has an integer stoichiometry. e) Bi-bi enzyme reaction. In this example, two molecules of identical type act as reactants and also as products, respectively. f) Arbitrary enzyme reaction. This reversible reaction involves a feedback inhibition and a complex stoichiometry, in which an ion and two identical molecules are created from two distinct reactants. g) Integer stoichiometry. This reversible, enzyme-catalyzed reaction has two identical reactants and one product. h) Irreversible reaction. This reaction has no explicit catalyst assigned to it. Depending on user-settings, the algorithm can still consider this an enzyme-catalyzed reaction, assuming that the omission of the catalyst is for the sake of simplicity. i) Modulated reaction. Both, a stimulator and an inhibitor interfere with this reaction. j) Reversible reaction. This dissociation reaction can also be seen as an association when the equilibrium shifts to the reverse reaction. k) Zeroth reactant order reaction. The two product molecules lower the velocity of their own creation. l) Zeroth product order reaction. The reactant stimulates its own degradation