However, we report here that orthologous pairs of TF DBDs almost invariably bound to the same DNA sequences, indicating that the binding specificity is very deeply conserved.
The location and the primary sequence were conserved in almost all class D CID members (Fig. 8), which suggested that binding specificity is highly related in all members of the class.
This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences.
Similarly, an A/T-rich consensus was found in L. kluyveri, L. waltii, S. paradoxus, and S. bayanus [ 5, 6, 21], proving that ORC/MCM binding specificities are also conserved over larger evolutionary distances.
This autosome-specific binding is conserved in evolution, as demonstrated by the F element specificity (also detected, for instance, in Drosophila pseudoobscura and Drosophila virilis).
Consistent with the importance of guanine nucleotide binding for septin function, our analysis showed that the G1 GTPase motif, which forms the loop that interacts with the phosphate group of the nucleotide, and the G4 motif, which is important for GTP-binding specificity, were highly conserved, with 154 of 162 (95%) septins matching the respective consensus sequences (see additional file 1).
Actin binding specificity was demonstrated by competitive binding experiments and comparative staining of well-known structures.
The presence of the highly conserved motif "EPN" and "WND" in the CTLD of PdC-Lectin argues in favour of the specificity for mannose binding in a Ca2+-dependent manner [ 53] and the molecular model obtained using the MODWEB server reveals that all residues involved in this binding specificity are located in similar predicted structures by comparison with the human DC-SIGNR CRD.
This indicates that even though the binding location of DB00631 fluctuates with different peptides, the overall binding affinity is conserved.
All positions are not highly conserved; however the hydrophobic nature of the binding site is conserved.
