To find the conserved DNA-binding motifs for each group of orthologous RhaR regulators , we used initial training sets of genes that are co-localized with rhaR orthologs ( putative operons containing at least one candidate L-Rha utilization gene and that are located in the vicinity of a maximum ten genes from a rhaR gene ) , and then we updated each set by the most likely RhaRregulated genes confirmed by the comparative genomics tests as well as functional considerations ( i.e. , involvement of candidate target genes in the L-Rha utilization pathway ) .