The evolutionary divergence among the three major domains of life can now b
e addressed through the first set of complete genomes from representative s
pecies. These model species from the three domains of life, Haemophilus inf
luenzae for Bacteria, Saccharomyces cerevisiae for Eukarya, and Methanococc
us jannaschii for Archaea, provide the basis for a universal functional cla
ssification and analysis. We have chosen 13 functional classes and three su
perclasses (ENERGY, COMMUNICATION and INFORMATION) as global descriptors of
protein function. Compositional comparison of the three complete genomes r
eveals that functional classes are ubiquitous yet diverse in the three doma
ins of life. Proteins related with ENERGY processes are generally represent
ed in all three domains, while those related with COMMUNICATION represent t
he most distinctive functional feature of each single domain. Finally, func
tions related with INFORMATION processing (translation, transcription, and
replication) show a complex behaviour. In Archaea, proteins in this supercl
ass are related with proteins in either Eukarya. or Bacteria, as recognized
previously. The distribution of functional classes in the three domains ac
curately reflects the principal characteristics of cellular life forms.