In ϕ24B, there is a single nucleotide change in this repeat in the same locations, but the GAD operon had no matches to either of the CII binding sequences, suggesting that the substantial effect of CIIϕ24B on acid resistance is pleiotropic.
On one hand, the use of RGD analogues resembling the integrin binding sequence suggested that 29-kDa and 50-kDa FN-fs exert their effects independently of integrin interactions [ 31].
Additionally, bioinformatic studies showed that each of these open reading frames contained a putative ribosome binding sequence, suggesting that they are translated as independent polypeptides.
Despite these nonrandom distributions, we could not identify a consensus binding sequence, suggesting that ORC1/CDC6 binding in the VSG arrays, like in the core, is not a sequence-specific feature.
These previously identified NAC binding sequences including their core binding motifs are not present within the identified ATAF2 binding sequence, suggesting that ATAF2 recognizes a binding sequence different from that used by other NAC proteins.
Finally, it is worth noting that ~10% of p63 ChIPed sites in keratinocytes do not have a recognizable p63 binding sequence suggesting that the p63 binding at these sites is driven by indirect mechanisms that might involve other DNA-binding TFs and/or non-canonical p63 motifs.
The lack of known functional domains, such as ATP-binding domains, selectivity pores, or G-protein-binding consensus sequences, suggests that either the ODP family has a novel function that significantly differs from the activities of known channels, transporters, or receptors, or that the ODP genes encode novel functional motifs.
Although ncRNA-mediated interactions linking REST to PRC2-bound chromatin have been proposed (Tsai et al., 2010), the strong correlation between REST-binding and RE1 DNA sequences suggests that any alternative mechanisms of stable recruitment to chromatin were not prevalent in ESCs.
Furthermore, these charged amino acids are highly conserved in available cytoplasmic dynein sequences, suggesting that binding at AAA3/4 is likely to be a common feature of Lis1-dynein interactions.
The circular dichroism changes in the Tmod upon binding and modeling of the Tmod sequences suggest that the interface between TM and Tmod includes a three- or four-stranded coiled coil.
