Figure 3.

Length and percentage identity of alignments of unrelated proteins in pdb90d-b: Each pair of nonhomologous proteins found with ssearch is plotted as a point whose position indicates the length and the percentage identity within the alignment. Because alignment length and percentage identity are quantized, many pairs of proteins may have exactly the same alignment length and percentage identity. The line shows the hssp threshold (though it is intended to be applied with a different matrix and parameters).