Swaps in protein sequences

ABSTRACT An important question in protein evolution is to what extent proteins may have under-gone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolution of proteins, and has practical implica-tions for using swaps as a design tool in protein engineering. In order to analyze the question system-atically, we conducted a large scale survey of pos-sible swaps and permutations among all pairs of protein from the Swissport database. A swap is defined as a specific kind of sequence mutatio