Alignment paths from 6 methods including reference positions. The x-axis corresponds to the residue positions in the backbone of one of the structures and the y-axis corresponds to the residue positions in the second structure. Aligned fragments are shown as lines with symbols at start and end of the aligned fragment pairs. Single aligned residues are plotted as symbols. The alignment of each method is represented by a specified symbol, line style and colour code. Reference positions are shown as red circles. A: Alignment plot of TIM barrel domains d1b5ta and d1k87a2. The different alignments result from the repetitive motifs in the TIM barrel fold and from the circular permutation. B: Signal peptidases d1ay9b_ and d1b12a_. There is a large insertion in the Type I signal peptidase d1b12a_. C: Alignment plot of P-loop containing NTP hydrolases d1jj7a_  and d1lvga_ . There are many indels of different sizes in the alignments.