First, computationally extensive analyses, such as full enumeration of elementary modes for metabolic pathway analysis, may only be tractable in smaller models.
Horizontal gene transfer (HGT), which is prominent among prokaryotes, allows for a different mode of metabolic evolution, where enzymes tend to be transferred in groups which are functionally coupled.
Algorithms for calculating elementary modes from metabolic network topology are described elsewhere [ 46].
Reliable kinetic modes of metabolic networks will accelerate drug target identification and rational drug development.
Minimal cut sets (MCS) represent "elementary failure modes" of metabolic networks [ 5].
Figure 1 shows how production of the electron transfer (MET and DET modes) competes with biomass production for metabolic resources.
Elementary mode (EM) analysis is ideally suited for metabolic engineering as it allows for an unbiased decomposition of metabolic networks in biologically meaningful pathways.
The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis (Schuster et al., 1999).
Motivation: The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis.
For metabolic networks for which elementary modes [ 11] or extreme pathways [ 12, 13] can be calculated, such higher-level descriptions of the solution space may provide fast alternatives to the constrained-based algorithms implemented in sybil.
