FIG. 3.

Independently optimized hierarchies for PRTaseII-related domains (cd00516). (A) A hierarchy optimized starting from a heuristically generated hierarchy. (B) A hierarchy optimized starting from a single root node (i.e., de novo). This (highest scoring) hierarchy serves as the reference for the other two hierarchies. (C) A hierarchy optimized starting from a manually curated hierarchy. Nodes in each full hierarchy are colored as indicated in Figure 2, but with some of the nodes in (B) two-toned to indicate that each of those nodes differs in correspondence with a node in (A) (top color) versus a node in (C) (bottom color). These three hierarchies share five subtrees in common (although utilizing distinct arrangements thereof). Each of the root nodes of these subtrees is highlighted in the full hierarchies with glow that is similarly colored as is the corresponding node in the truncated hierarchy below. These subtrees are investigated further here. For the truncated hierarchies, the LLR contribution (in nats) to the subhierarchy [i.e., subLLR(H^h), where h corresponds to the associated node] and to the contrast alignment [i.e., subLLR(h)] are indicated by the numbers shown in black and red, respectively.