Scheme 1.

Structural contacts mapped into M-long multi-sequence alignment (MSA) of protein interologs A and B. A set of pairwise protein-protein interactions is defined by associating each sequence l in MSA B to a sequence k in MSA A in one unique arrangement, {l(k)|z}_M, determined by the coevolution process z to which these protein families were subjected. Shown is a “scrambled” concatenated MSA of A and B associated to a given process z (red dashes). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)