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Although convergent evolution exists, a recent study indicated that domain convergence and multiple domain genesis are rare and most domains emerged only once during evolution [11].
Moreover, HGT or multiple domain genesis events can give rise to the same apparent domain distribution patterns on the tree of life and hence are not distinguishable (see supplementary Text S1).
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Domain genesis indicates the origins of protein domains.
Therefore, the penalty score for either domain genesis or HGT is defined as Rhgt (Rhgt>1), indicating the relative likelihood of domain genesis or HGT with respect to loss.
Four evolutionary processes govern the presence or absence of a domain at each node in the tree: vertical inheritance, domain loss, horizontal gene transfer (HGT) and domain genesis.
Four evolutionary processes, vertical inheritance, domain loss, horizontal gene transfer (HGT) and domain genesis can change the status of domain content.
As Rhgt increases, the number of domain genesis events falls to 0, which means every domain/combination was only invented once in history with no HGT and no convergent evolution.
We find 11 new multiple domain proteins.
The 3' terminal exon encoding the AKAP7 RI/RII binding domain first appears in the AKAP7 gene of lamprey and is conserved throughout vertebrates, placing AKAP7 binding domain genesis at the base of the vertebrate lineage.
Tap is a multiple domain protein composed of a Lotus domain and three Tudor domains.
Understand the value of multiple domain names.
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