Figure 3

Effects of structure and sequence variation on the alignment. The bottom panel shows structural difference (measured by the RMSD) versus alignment similarity, measured by the SP score, which is defined as the fraction of aligned reference residues pairs that are reproduced in the query alignment. The top panel shows distributions of SP scores for alignments sharing less and more than 50% sequence identity. Orange (lighter) refers to alternative crystal structures while blue (darker) refers to alternative structures obtained from molecular simulations.