Example of the types of similarity considered in this study. The protein at top left (enterotoxin, PDB code 1lts-d) is similar in 3D structure to all of the other proteins in the figure.
The similarity with cholera toxin (1chp-d; top right) is a close homology, since structure/function similarity is accompanied by a high sequence identity (80%).
The second similarity, with toxic shock syndrome toxin (TSS; 1tss, bottom left) is accompanied by a functional similarity, but no significant sequence similarity (8.8%) and is thus classified as a remote homologue.
The third similarity, with a domain from aminoacyl tRNA synthetase (1krs; bottom right) is accompanied neither by any significant sequence similarity (4.4%) nor any functional similarity, thus classifying it as an analogue. More details can be found in the paper.
Magenta regions in the three structures on the right show those regions that are structurally equivalent with enterotoxin (top left).