Distribution of reference alignments over sequence similarity. The sequence similarity is the fraction of identical residue pairs among all aligned pairs. The fraction of sequence pairs (solid lines) and residues pairs (dashed lines) are plotted in each range of sequence similarities for the root (black) and the terminal (red) node sets. The terminal node set includes 2,199 alignments and 288,401 aligned residue pairs. The root node set includes 4,017 alignments and 245,817 aligned residue pairs. The x-axis gives the mid-point of the similarity range bins of size 0.1. The distribution of the residue pairs is slightly shifted to the right compared to that of the sequence pairs. This implies that there are some large structures with high sequence similarity.