Genomic context of genes associated with xylose and xyloside utilization in Firmicutes. (A) Examples of chromosomal clusters and putative regulons containing genes involved in xylose and xyloside utilization. Candidate regulatory sites of XylR from ROK family are shown by red circles. Genes predicted by genome context analysis are marked by asterisks. Homologous genes are marked by matching colors. (B) Phylogenetic tree and (C) DNA recognition motifs of XylR including all known and predicted xylose regulators from Firmicutes. XylR proteins recognizing the same DNA motif are grouped, and the corresponding motif sequence logos are shown in (C).