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For these functions, the chaperones need to exhibit a significant promiscuity in binding to different sequences of hydrophobic peptide stretches.
We do not observe significant differences between Elk1 and Elk4 DNA-binding specificity in either of the independently performed DNA-binding specificity assays, suggesting that the differences in binding observed earlier were related to changes in overall affinity of the ETS factors to DNA as opposed to effect on specificity of binding to different sequences.
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Further problems of promoter predictions consist in the existence of different sigma factors binding to different recognition sequences and in the variation between the consensus sequences of different bacterial species.
Maximal spore heat and nitrite resistance required production of all four C. perfringens Ssps, indicating that these Ssps act cooperatively to protect the spore's DNA, perhaps by binding to different chromosomal sequences.
To take this possibility into account, a more sophisticated assumption can be applied; that is, TFs can have different binding preferences to different sequences or under different experimental conditions.
Note also the red rectangles off the diagonal, indicating that although the homeodomain proteins binding to different motifs have high sequence similarity, the motifs themselves are divergent.
Despite their high overall homology (approximately 75% identity at the amino acid level), the BRG1 and BRM sequences diverge at the N-terminal region; these sequences regulate their binding to different transcription factors, and they form mutually exclusive SWI/SNF complexes.
NF-κB dimers bind to different κB sequences with different binding affinities and binding modes.
One can envision that such combinatorial usage of multiple quasi-independent sites can in principle generate a large repertoire of binding targets with different sequences for ANK repeats.
We compared our PBM model with seven other methods that predict affinities of TF binding to given sequences, and the different methods are evaluated using areas under the ROC curve (AUC) as a measure of their abilities to correctly classify the two sets of sequences (see Methods, Supplementary Results in Additional file 1 and Figure S1 therein for details).
The affinity difference between human and cynomolgus monkey RGMc could be due to the different sequences in the binding epitopes of ABT-207 between these two species.
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