It is clear that these three p53s evolved independent of the vertebrate p53, p63 and p73 although it is surprising that Nematostella p53 DNA binding domains are more closely related to vertebrates as compared to worm and fly p53 like proteins, a feature shared with many other proteins [ 28].
This phenotype, reminiscent of cep-1, together with the p63 DNA binding domain being more closely related to cep-1 lead to the notion that p63 might be the closest mammalian CEP-1 homolog.
For both proteins, functional presentation of cell-binding domains was more effective on the more hydrophilic 100%OH-SAMs.
Finally, genome-wide functional profiling of spliced-out domains has revealed that a number of domain types, e.g. protein-binding domains, are more frequently spliced-out by AS than expected by chance [ 19].
Also, we utilized an additional criterion of similarity between candidate site motifs for closely related regulators that is based on the expectation that binding sites of regulators with closely related DNA-binding domains are more likely to be at least partially similar [ 21, 31- 33].
However, modifications in the heme-binding domain are more frequently found in CYPs with catalytic activity, often not requiring oxygen, and may indicate novel catalytic activities in these exceptions (Song et al. 1993; Li et al. 2008; Kelly et al. 2009).
In comparison with RNA-binding motifs, auxiliary domains are more divergent in amino acid sequence and structure, making it difficult to classify.
Then the ligand binding domains were extracted from the alignments.
Since many repeated domains have binding functions, it is also reasonable that these proteins have more connectivity than single domain proteins and hub proteins with repeated domains are more probable than non-hubs in network.
Multifunctional protein binding domains are domains which can recruit more than one binding partner.
