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Select a reaction combination and generate a list of all accepted fragments for the combination using the PieceMaker API (application programming interface) (Stenberg et al., 2005a ).
The combinatorial nature of the pairwise input/output reaction combination for each metabolite is the key to the exponential growth of the number of modes during the execution of the algorithm.
Also, the time required to generate and evaluate fragments will increase linearly with the number of reactions, while the time required to select a reaction combination will increase with the number of possible reaction combinations, which depends on both the number of reactions in the pool, and the maximum number of reactions allowed.
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This suggests that evolution of metabolic networks is governed by reaction combinations that are favoured by natural selection.
Specifically, is it caused merely by natural selection favoring certain reaction combinations, or do metabolic reactions also co-vary in their transfer from bacterium to bacterium?
Each set of validation experiments comprised at least four reaction combinations (T related to C) with three replicas for each point in the conditions described above.
Even a limited number of available genomes suffices to show that metabolic network evolution is highly constrained by reaction combinations that are favored by natural selection.
In other words, if certain reaction combinations are favorable, then the genes involved in them might become tightly linked over time.
A reaction in this table represents a potential connection within the metabolic network, while the existence of a link in a certain organism is indicated by a value greater than or equal to unity for each organism-reaction combination.
8 In these reactions, combinations of halide, oxygen, and nitrogen nucleophiles are added across the diene.
For lumped reactions (the combination of multiple sequential reactions into a single overall reaction), γ denotes the number of irreversible steps and γ=1 for individual reactions.
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