Figure 3.

Clustering of the database. (a) Domain d1jnfa2 [33], a periplasmic-binding protein-like II (c.94) domain, was selected for this example. (b) Schematic representation of the 12 alignments in which d1jnfa2 appears. Domain d16vpa_ is represented as a maroon box. Below appear the other domains ordered by their start position. SCOP families and probabilities are stated for each domain. Sequence positions where each alignment starts are depicted relative to d1jnfa2's sequence (20, 35, and 185). The coloring scheme is the same as in (c), where each alignment has been plotted according to start and end position. The length of each fragment is thus the distance to the diagonal. The 12 sequence regions were combined into three clusters, depicted within the d1jnfa2's structure.