Visualizing metabolic pathways: comparative genomics and expression analysis

As a large number of genomes are sequenced, interest turns to the functions and dynamics of the identified genes and how these influence the physiology of the organisms. Many genes code for enzymes that catalyze metabolic reactions producing energy and various molecules that constitute the core activities of the cell. Most of these reactions occur in a step-wise manner involving several enzymes and intermediates, and these can be portrayed graphically in the form of metabolic pathway maps. The ability to collect information en masse about expression profiles provides an opportunity to study the regulation of individual enzymes as well as of the pathways in which they exert their function. This article describes two integrated databases of metabolic pathways and genomes, available via the internet. We discuss how the analysis of metabolic pathways can provide support for the determination of gene functions, for comparisons of cellular networks and for the design of novel antimicrobial drugs.