Figure 3

ProfileGrids highlighting differences between AKL alignment subpopulations. The JProfileGrid software offers many user defined options to customize the appearance of the ProfileGrid for final figure export here shown for the AKL alignment across all organisms for 1,809 sequences (A), from Gram negative bacteria for 923 sequences (B), and from Gram positive bacteria for 886 sequences (C). The ProfileGrid panel first row shows the consensus sequence from the Gram negative (B) and Gram positive (C) alignments while panel (A) shows the majority residues from the entire MSA. The pink boxes in panels (B) and (C) highlight differences between the two consensus sequences shown. For each panel, the color shading is normalized to the number of sequences in each alignment as a grayscale ramp from white (<10%) to black (>= 90% conservation). For clarity, the ProfileGrid cells in panels (B) and (C) do not show any values or symbols to facilitate visual inspection of the patterns. The residue codes in the panel (A) second column are color shaded to represent the following amino acid classes: hydrophobic (brown), basic (blue), nitrogen-containing (lavender), acidic (red), and other (green). The ProfileGrid rows are sorted according to the amino acid classes whereas in Figure 2 the rows are sorted alphabetically by residue symbol.