Impact of domain shuffling on domain architecture (top).

<p>Each point plots the minimum and maximum domain frequency in a protein. For example, the original domain set for protein 949, D(949) = {PBD, Pfam-B_2441, Pkinase} (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088943#pone-0088943-t002" target="_blank">Table 2</a>). The minimum and maximum occurrence values for D(949) are 1 and 5 respectively. A point (x, y) in the plot denotes the minimum and maximum domain occurrence in a protein. Prior to domain shuffling, there are proteins with both rare and promiscuous domains, as shown by the black markings in the upper left of the plot. After domain shuffling, proteins have domains which are either rare only or promiscuous only, as shown by the orange markings on the y = x line. Domain shuffling changes the original heterogeneous domain architecture to a homogeneous one in terms of domain occurrence. <b>Gold domain coverage by protein type after domain shuffling (bottom).</b> At all rare domain threshold values, at least 99.5% of the 642 gold domains are covered by either proteins comprising only rare domains or proteins comprising only promiscuous domains. When the rare domain threshold is 4, the coverage comes very close to a 50∶50 split. Compare with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088943#pone-0088943-g005" target="_blank">Figure 5</a> (bottom) for gold domain coverage by protein type before domain shuffling.