The UA9 motif logo (supplementary fig. S5 B and C, Supplementary Material online) was previously associated with TF-binding events of multiple regulatory proteins exclusively in H1-hESCs, including NANOG, BCL11A, HDAC2, ESR1, GATA2, RXRA, TCF12, and a subset of HDAC2-associated POU5F1-binding sites (Wang et al. 2012).
In total, we collected 255 nuclear-encoded plastid proteins from our data set with a full-length 5′ end encoding a BTS, from which we generated a sequence logo (fig. 1; supplementary table 2, Supplementary Material online).
These high quality PWMs and their associated sequence logos are in Supplementary data Figure S5.
Their motif logos are in the supplementary Table S2.
They are also listed at the bottom of Table 1, and their logos are listed in supplementary Table S3 together with the corresponding TRANSFAC TFBSs that are most similar to.
The motif sequence logo is available in the supplementary material (Additional file 18).
The details of sequence logo of motifs were shown in Supplementary Fig. S1.
Beta-barrel outer membrane proteins for members of several distantly related Phyla, to cover a wider range of the bacterial diversity, were predicted starting from all annotated open region frames for the respective organisms (supplementary fig. S7, Supplementary Material online), and logos were constructed for the C-terminal 15 amino acids from these protein sets.
Ten TFBSs satisfy this criterion and they are listed in Table 1 (their corresponding motif logos are given in Table S1 in Supplementary Materials).
The sequence logo representation of these alignments is provided in Supplementary Figures 2 9.
According to the annotations of kinase families in KinBase, the data statistics of kinase-specific phosphorylation sites in different species, as well as the sequence logo of kinase substrate motifs, were presented in Supplementary Table S4.
