The differences between single pathway-based treesand 16S rRNA-based trees. (a) In the 16S rRNA-based tree, two γ-proteobacteria Buchnera aphidicola (Buc) and Escherichia coli (Eco) are clustered together. In the phylophenetic tree based on the topology of the glycolysis/gluconeogenesis (map00010), the obligate intracellular symbiont B. aphidicola (marked with red color) is clustered with the obligate intracellular parasite M. pneumoniae (Mpn), mainly due to the gene loss in the two organisms. (b) In the 16S rRNA-based tree, two archaea Halobacterium sp. NRC-1 (Hal) and Aeropyrum pernix (Ape) are clustered together. In the phylophenetic tree based on the topology of the selenoamino acid metabolism (map00450), Halobacterium (marked with red color) is clustered with actinobacteria Streptomyces coelicolor (Sco), mainly due to the putative horizontal gene transfer of selenocysteine lyase.