Table 4 Reaction categories. This table lists and describes reaction categories with relevance to automatic rate law assignment. Graphical examples for each category can be seen in Fig. 2. These categories are not mutually exclusive. A reaction can therefore belong to multiple categories. Similarly, all available rate laws are also assigned to these categories (see Table 5). Since also each rate law can belong to multiple categories, some of these categories are used to refine the selection of rate laws for a reaction, i.e., some categories are exclusive. A rate law may belong to the category of reversible (J) and irreversible (H) reactions if it is possible to apply the rate law to both types of reactions, but a rate law from category G can only be applied to a reaction in which all participants have a strictly integer stoichiometry. Rate laws that have mechanisms for modulation can also be applied to non-modulated reactions, but rate laws that do not belong to category I cannot be applied if activators or inhibitors interfere with the reaction
From: SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
\({\text {N}}^{\underline {o}}\) | Category | Description |
|---|---|---|
A | Non-enzyme reactions | Spontaneous reactions and reactions with a catalyst that is no enzyme. |
B | Gene-regulatory processes | Reactions that produce RNA or produce polypeptide molecules from an empty set of reactants or whose reactants are genes or RNA molecules and that have genes or RNA molecules as modifiers. |
C | Uni-uni enzyme reactions | Enzyme-catalyzed reactions with one reactant of stoichiometry one and if reversible also one product of stoichiometry one. |
D | Bi-uni enzyme reactions | Enzyme-catalyzed reactions with two reactants, i.e., an integer stoichiometry two on the reactant side, and if reversible one product of stoichiometry one. |
E | Bi-bi enzyme reactions | Enzyme-catalyzed reactions with two reactants, i.e., an integer stoichiometry two on the reactant side, and if reversible two products that also have a stoichiometry of two. |
F | Arbitrary enzyme reactions | Enzyme-catalyzed reactions with an arbitrary number of reactants and products. |
G | Integer stoichiometry reactions | Reactions whose participants have only integer stoichiometric values. |
H | Irreversible reactions | Reactions whose net flux proceeds only in forward direction. |
I | Modulated reactions | Reactions whose velocity is influenced by modifiers, such as activators (stimulators), inhibitors, an (enzymatic) catalysts |
J | Reversible reactions | Reactions that can proceed in forward and reverse direction. |
K | Zeroth reactant order reactions | Reactions in which the effects of reactants do not contribute to the velocity. |
L | Zeroth product order reactions | The effects of products do not influence the velocity of these reactions. |