Instead of the description only, GOOD further provides the GO graphs to reveal hierarchical-like relationships among divergent functionalities.
Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities.
Our results, when combined with those of others [ 10, 6], imply that the methylation level at the 12th position of CTCF binding sequence may alter the binding environment, resulting in different zinc-finger binding and, in turn, recruiting different cofactors that ultimately leads to divergent functionalities.
These results support the accuracy of our identification methods, provide evidence that the Pfam HMM for the CydX family is too stringent, and suggest that CydX homologues retain a similar functionality among divergent species.
Taken together, this study's findings indicate that small transmembrane proteins are widespread members of the cytochrome bd oxidase complexes in Proteobacteria, that these proteins share a common functionality across divergent homologues, and that CydX and convergent small proteins may act in concert with the CydA Q-loop in the activity of the membrane-bound oxidoreductase.
In order to quickly test the functionality of the divergent MAT1-2-1 H allele, we attempted to provoke selfing in strain H327.
Further, the divergent FAD2 enzymes with novel functionality could be used to produce rare fatty acids, such as crepenynic acid, in genetically engineered crop plants that are precursors for economically important phytoalexins and oleochemical products.
Thus, CTCF could be a "dual functionality" protein that has divergent effects on different gene regulation systems.
However, it is possible that whilst a conserved signal transduction pathway exists, these pathways are divergent at the MAP3K level of functionality: humans employ MAP3K1 (and presumably other interacting molecules) to regulate this pathway, but there are no reports of mutations in MAP3K4 causing human DSDs.
