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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.
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Furthermore, two distinct ER isoforms exist which have divergent functionality as well as tissue- and cell type-specific expression.
This tandem duplicated cluster may have similar or divergent functionality and/or regulation, and may underlie the differences seen in drug metabolism in the pig.
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.
Two alternative explanations were suggested for these observations: (1) a copy of the gene in the nucleus had gained functionality; or (2) at least one of the highly divergent rpoA-like ORFs remains functional.
Thus, CTCF could be a "dual functionality" protein that has divergent effects on different gene regulation systems.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com