Pathway Analysis for Metabolic Engineering
The term metabolic engineering implies analysis of metabolic states and rationally designing the pathway and predicting changes. For this purpose, appropriate tools are required which include the following : (i) metabolic flux balancing; (ii) metabolic control theory and (iii) optimization methods. In general there are two main approaches to metabolic engineering. In the first approach, either some enzymes can be blocked completely or removed by knocking out the corresponding genes, or else genes for new enzymes can be inserted, thus changing the topology of the reaction network. In the second approach, enzyme activities can be changed gradually or regulatory interactions can be altered. This needs much more extensive data and sophisticated theoretical tools, because complex kinetic information is involved.

A flux mode is defined as a steady-state flux distribution, in which the proportions of fluxes are fixed. For example in, SI is the substrate, from which x units of flux might go through reactions 1 and 2, while y units of flux are carried through reaction 3 and 4 (ratio of x and y specified). However the physical units of flux will remain unspecified unless measured flux data are available. A flux mode is called elementary, if it is non-decomposable. In, reaction I and 2 make one elementary mode and reactions 3 and 4 make another elementary mode and the two elementary modes do not overlap, although generally elementary modes do overlap (the product of one becomes substrate of another reaction).

Generally speaking, an elementary flux mode is a minimal set of enzymes that can operate at steady state, with all irreversible reactions proceeding in the direction prescribed thermodynamically. Following theoretical approach may be followed for the sake of defining elementary mode, (i) start from a given metabolic system; (ii) block an enzyme by addition of an excess amount of enzyme inhibitor and examine if there is still some flow through the system; (iii) block a second enzyme and so on. An elementary mode is reached, when further inhibition leads to cessation of any steady-state flux. The set of genes that can be deleted simultaneously is termed the Dispensable set.