In our study, motif 6, 7, 8 and 20 appeared in the group A VvbZIP exclusively and they widely represent the potential phosphorylation sites described above.
Taken together, this information shows that type I-C seems to have a constant PAM and is a suitable type to study motif underrepresentation across different bacterial species.
Nevertheless, a similar analysis performed on a set of 53 co-regulated genes responding to PAA in the lab strain Wis54-1255 and the DS17690 strain (cluster 1, described in [ 17]) identified the same motifs as found in the present study (motif 1 from group 1 and motif 2 from group 7).
We also see two major features in the PC that sets apart the vertebrate and insect proteins - presence of CIPC motif in the insect protein and that of DNA binding AT-Hook or ATHL (identified in this study) motif in all vertebrate homologues.
In this study, motif 2, 5, 1, 3 and 6 specifying the NAM subdomain A to E respectively were present in most of the NAC family members in Populus, whereas a small subset of sequences did not have all five motifs in the typical NAC DNA-binding domains.
In other studies, motifs lead us humorously into the music and the choreography at the same time, like the advancing prance with opposite-pushing arms: This takes us into staccato scales in the music, both rising and falling, and the way successive dancers take it up is enthralling.
The most intensively studied motifs are derived from the consensus repeats of elastin and silk, as well as coiled-coil helices.
First, we studied motifs predicted by SIOMICS in random DHS datasets.
Correlations between main sequence features and recombination rates were investigated and significant correlations were obtained for all the studied motifs.
The BLS was first used in a comparative study with 12 Drosophila genomes (Stark et al., 2007) and allows studying motifs only conserved in subsets of the organisms.
