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Although the proline-rich region is not always conserved, the SH3 binding domain is conserved in the dsh-1 orthologs of all taxa, but is absent in nematode mig-5 orthologs.
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The AAAG binding domain was conserved in motifs Dof2, Dof3, PBF and MNB1A (DOF family) and was found specifically in triacylglycerol biosynthesis genes in our seed samples.
Amino acid motifs located outside the DNA binding domain are conserved among the Arabidopsis [ 8] and Vitis ERF proteins (Additional file 3, Table S3).
Although the putative GSH binding domain was conserved across all sequences in both the LigE cluster and the HypGST cluster A, sequence analysis revealed several dissimilarities between the two clades.
Interestingly, we found that only one intron 4 retention event (I4R) introducing PTCs downstream of their DNA binding domains is conserved between CCA1 and LHY homologs.
To identify whether the β-catenin-binding domain is conserved in all Xins or alternatively is a derived trait specific to mXinα, the homologous region to the mXinα's β-catenin binding domain for the other 39 Xins were identified and aligned (Figure S2).
In order to determine if a lack of Yap-Tead activity is responsible for RPE loss, we first tested whether the Yap and Tead binding domains are conserved in zebrafish.
Alignments of the full protein sequences of the orthologs revealed that the zinc-finger DNA binding domains were conserved as were two regions in the C-terminal domain, but otherwise there was a great degree of sequence divergence (see Additional files 1, 2 Fig. S1 for alignments of orthologs).
Half of the residues of the calcium-binding domain (Y-R) and eight residues out of 28 in the heparin-binding domain are conserved, which confirms that these domains are important.
Phosphotyrosine-binding domains are conserved sequences of 100-150 acids acidsubsetubset of which recognize the consensus sequence NPXpY [ 1].
These phospholipid-binding domains are conserved in class-4 coronins and are most probably responsible for their association with internal membranes like Golgi-structures and ER-membranes [ 34].
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