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The W-box is a WRKY binding motif, which is the specific binding site of a transcription factor family related to senescence and defense systems in plants.
In order to use TRANSMODIS, one has to supply a consensus binding motif, which is not always known in advance, especially in higher eukaryotic organisms.
The previously described C-terminal plasminogen binding motif, which is formed by two terminal lysine residues (KK) [23], [24], [27], was conserved in 34 of the 56 isolates, this excludes all 19 anginosus group strains and a S. salivarius strain (SV121) which all possessed a terminal SK instead.
Besides their size difference, BmBruce also has an ubiquitin-proteasome binding motif, which is homologous to Drosophila Bruce protein [ 66].
CYT-1, but not CYT-2, contains a PI3K binding motif, which is required for PI3K-Akt activation by ERBB4.
We further determined that the gene regulatory activity of CR4.2 is modulated by Meis1 binding motif, which is bound and activated by Meis1 transcription factor.
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Through MotifNetwork, we found that all 100 sequences have a glutamate binding motif, which was expected because we took glutamate binding region as our PSI-BLAST probe.
Indeed as shown in Figure 4 these proteins also have an identical adenine binding motif, which was also described by Denessiouk and Johnson [25].
The observed enrichment of SU HW) and the paucity of the other four insulator proteins in LADs could be dictated by the genomic distribution of the corresponding DNA binding motifs, which is likely since the presence of a SU HW) DNA binding motif is known to be highly predictive for SU HW) binding [38].
For instance, it was previously observed that the functional divergence of transcription factor gene duplicates in terms of their DNA binding motifs (which is directly encoded by the DNA binding domain) inversely relates to their expression divergence [ 13], underscoring the importance of domain-centric analysis of functional divergence of paralogs.
Drosophila Yorkie is missing the C-terminal PDZ-binding motif, which is necessary for the connection between YAP1/TAZ and tight junction (TJ) proteins in mammalian cells.
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