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This approach has been successfully applied to determine a binding motif for the chemokine receptor CXCR4.
The VP1 G H loop of the foot-and-mouth disease virus (FMDV) contains the primary antigenic site, as well as an Arg-Gly-Asp (RGD) binding motif for the αv-integrin family of cell surface receptors.
Hydroxyquinoline is known to possess a high affinity for Fe and was thus chosen as the Fe binding motif for the hexadentate chelators, C1 (2,2′-[ethane-1,2-diylbis iminomethylene 2,2′-[ethane-1,2-diylbis iminomethylene 2,2′-[ethane-1,2-diylbis iminomethylene 2,2′-[ethane-1,2-diylbis iminomethylene
Motifs cc_08, cc_10 and cc_11 share similarity with the binding motif for the CtrA cell cycle master regulator.
It has been reported that DLC1 Y442 and S440 form a phospho-independent binding motif for the SH2 domain of tensin1 and cten [27], [28].
Motif cc_7 is the binding motif for the SigT alternative sigma factor, and genes in this cluster have a distinct peak of expression at the swarmer-to-stalked cell transition (Figure 2B).
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Undoubtedly, many output domains constitute DNA binding motifs for the transcriptional regulation of genes.
We also found several putative binding motifs for the co-factors of DAF-16 in regulating lifespan.
Experiments on our test set suggest that de novo motif discovery is able to identify significant binding motifs for the vast majority of TFs.
One study has shown conserved specificity for DNA binding motifs for the transcription factor NF-κB from N. vectensis when compared with other animals [45].
Additionally, we have identified DNA binding motifs for the NAC and YABBY transcription factors.
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