The paper presents a method for predicting functional coupling between genes based on the conservation of gene clusters across multiple genomes. The authors use a computational approach, leveraging the WIT system, to identify conserved gene clusters and pairs of close bidirectional best hits (PCBBHs). They find that approximately 35% of genes assigned to known pathways appear in the same cluster with other genes from the same pathway. The method is applied to reconstruct metabolic and functional subsystems, such as purine biosynthesis and glycolysis, in various prokaryotic genomes. The results show that the presence of conserved gene clusters can accurately predict functional coupling, and the utility of this approach increases with the number of genomes analyzed. The authors conclude that the availability of multiple genomes is crucial for gaining insights into the processes that drive the formation and dispersion of chromosomal gene clusters, and that this method can support the assignment of functionality to uncharacterized genes in sequenced genomes.The paper presents a method for predicting functional coupling between genes based on the conservation of gene clusters across multiple genomes. The authors use a computational approach, leveraging the WIT system, to identify conserved gene clusters and pairs of close bidirectional best hits (PCBBHs). They find that approximately 35% of genes assigned to known pathways appear in the same cluster with other genes from the same pathway. The method is applied to reconstruct metabolic and functional subsystems, such as purine biosynthesis and glycolysis, in various prokaryotic genomes. The results show that the presence of conserved gene clusters can accurately predict functional coupling, and the utility of this approach increases with the number of genomes analyzed. The authors conclude that the availability of multiple genomes is crucial for gaining insights into the processes that drive the formation and dispersion of chromosomal gene clusters, and that this method can support the assignment of functionality to uncharacterized genes in sequenced genomes.