Fig. 2

Comparing stable structure retention and safety coverage (y-axis) for several sequence identity ranges between cluster members against the cluster representative (x-axis) carried out with EMERALD parameters \(\alpha = 0.75\) and \(\Delta = 8\) on all obtained sequences, where N denotes the number of sequences in each identity range. The dashed lines indicate medians and the dotted lines the first and third quartiles. The safety coverage increases with higher identity ranges due to the smaller size of the suboptimal alignment space for high identity sequence pairs. Since the stable structure retention quantifies the proportion of stable amino acids that are alignment-safe, it increases alongside an increase in safety coverage. The high stable structure retention results indicate that EMERALD is indeed able to capture biologically relevant stable positions, as they make up a higher proportion when restricting the sequence to safety windows. a All sequences are included (i.e., with safety coverage of at most 100%). b Sequences restricted to those having safety coverage of maximum 80%