FIGURE 2.

YbaB_cc is conserved across multiple bacterial species. (A) Multiple sequence alignment of YbaB/EbfC proteins from different bacterial species using MultAlin software (red—high consensus residues, blue—low consensus residues, at the given position). (B) Structural superposition of the modeled YbaB_Cc protein with structural homologs. The modeled protein (colored green and shown in cartoon representation) is a homodimer, as seen in the structural homologs from E. coli (PDB id: 1PUG) colored light blue. Another structural homolog from Haemophilus influenza (PDB id:1J8B) colored magenta is in monomeric form. Image made using PyMOL. (C) Protein-DNA docking model of YbaB_Cc (shown in cartoon and surface representation colored in secondary structure) is observed to bind to the DNA motif (5′-ATGTAACAGCTGAATGTAACAA-3′) as obtained from HADDOCK web server. The insets show the orientation of side chains of the interacting residues in stick representation (colored cyan). (D) Schematic representation of the ybaB/ebfC gene locus with adjacent genes in various bacteria. This arrangement of genes appears to be conserved in most bacteria that harbor YbaB/EbfC proteins. (E) YbaB homologs in alpha proteobacteria. Genomes displaying YbaB homologs with more than 40% sequence identity are labeled in red and proteins having identity below 40% are labeled in orange. Bacterial genomes with no YbaB homologs are labeled in yellow.