Figure 5

Three highly constrained reactions (P < 10^-20) in the histidine utilization pathway. a) shows the three first reactions of the histidine utilization pathway, color-coded to help visualize their occurrence in b), which displays a 16S rDNA-based maximum-likelihood phylogenetic tree, visualized by ITOL [101], of the bacterial species analyzed here. Bars along the circumference of the tree indicate whether a specific reaction (as indicated by the bar's color) is encoded by a genome or not. Bars containing two or more colors indicate that the respective reactions are encoded in two or more genomes. Note that most bars contain all three colors, indicating that the respective genomes encode all three reactions. c) shows the distance in kilobase pairs and d) the number of genes intervening between genes encoding histidine ammonia lyase and imidazolone propionase in the studied genomes. The bimodality of the distributions in c) and d) is similar for the other reaction pairs (not shown), with a bias towards tightly linked genes. The fourth reaction (formiminoglutamase) shown in a) is not part of a highly constrained reaction set significant at P < 10^-20. However, it is associated with the remainder of the pathway. For example, it is associated with the imidazolonepropionase reaction preceding it at P < 10^-8. Whereas 84 genomes encode imidazolonepropionase, only 38 of them encode a known ortholog of formiminoglutamase, which is responsible for the weaker association. (37 of these 38 genomes also encode the imidazolonepropionase reaction.)