FIG. 7.

A hierarchy of contrast alignments revealing pattern residues. (A) The path from the root to node 14 in PRTaseII hierarchy B. (B) Pattern residue structural locations within Mycobacterium tuberculosis quinolinate phosphoribosyltransferase in complex with phthalate and a substrate analog, PRPCP (1QPR) (Sharma et al., 1998). The highest scoring pattern residues in (C) are shown. (C) Contrast alignments associated with the root and with nodes 48 and 47. Representative aligned sequences (which were assigned to node 14) are highlighted to reveal pattern residues; the red dots indicate the residues shown in (B). Foreground and background residues at each position are shown below each alignment, and directly below these, corresponding frequencies are given in integer tenths (a “7,” for example, indicates 70–80% conservation). The bar height above each highlighted column j corresponds to subLLR(j,h).