Toward understanding the origin and evolution of cellular organisms

Abstract

In this era of high-throughput biology, bioinformatics has become a major discipline for making sense out of large-scale datasets. Bioinformatics is usually considered as a practical field developing databases and software tools for supporting other fields, rather than a fundamental scientific discipline for uncovering principles of biology. The KEGG resource that we have been developing is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is now one of the most utilized biological databases because of its practical values. For me personally, KEGG is a step toward understanding the origin and evolution of cellular organisms.

Keywords: KEGG; KEGG MEDICUS; KEGG module; pathway mapping; reaction module.

Figure 1

The KEGG metabolic pathway map for arginine biosynthesis (map00220), where rectangles and circles represent enzymes and chemical compounds (substrates and products), respectively. Enzymes are identified by functional orthologs called KOs, although EC numbers and gene names are displayed. The KEGG pathway module is a functional unit in the metabolic pathway defined by a set of KOs. Two modules M00028 (upper) and M00763 (lower) are shown by pink‐colored rectangles

Figure 2

The global map of metabolic pathways (map01100), which contains 3,000 chemical compounds and 4,000 enzyme KOs. The coloring distinguishes categories of metabolic pathways as defined by KEGG. The arginine biosynthesis pathway of Figure 1 is highlighted with thick red lines

Figure 3

Correspondence of pathway modules (M numbers in green) defined by KOs and reaction modules (RM numbers in blue) defined by RCs. Reaction modules are more general functional units, each of which may correspond to multiple pathway modules, such as RM001 for 2‐oxocarboxylic chain extension and RM002 and RM033 for conversion to basic and branched‐chain amino acids, respectively