Annotations of domain swapping events. Aligned domains are shaded in light gray while unaligned domains are shaded in dark gray. All cases of unaligned domains are given one of five annotations. 1) Segment duplication/deletion. A segment of two or more domains were duplicated adjacently, or was lost. 2) Repetition difference. The first protein has one more B domain than the other protein. Since the unaligned domain is located next to an aligned domain of the same type, the unaligned domain is annotated as a repetition difference. 3) Insertion/deletion of a new domain. The first protein has two unaligned B domains. Both of these domains will be annotated as insertion/deletion of a new domain, since the other protein lacks domains of that type. 4) Insertion/deletion of an existing domain. The first protein has two unaligned A domains. Since the other protein has a domain of that type, the unaligned domains in the first protein will be annotated as insertion/deletion of an existing domain. 5) Domain shuffling. Both proteins have unaligned B domains. None of these domains occurs next to an aligned B domain and therefore they cannot be annotated as repetition differences. These domains will instead be annotated as exhibiting domain shuffling.