The first motif has an Ile-Val substitution while the second motif has a Leu-Val substitution, neither of which are substitutions with large effect on hydrophilic properties.
A horizontal band of enrichment around y = 0 shows that the first motif is enriched at the peakMax, while a band of enrichment on the diagonal is the second motif's enrichment at the peakMax.
For the second motif the amino acids at each position for several cleaved peptides was "added".
In the first motif, the middle five bases were the best conserved, while the first base T was the least conserved.
From the motif list in which the 16 motifs were sorted in ascending order of the p-values, we removed the 1st motif and, for each of the reminder, we calculated the KL distance from the first motif.
For each given sequence, the left plot reports the location of the first motif relative to the peakMax on the y-axis, and the location of the second motif relative to the first motif on the x-axis.
Mutation of CAC to GCG in the first motif resulted in a binding affinity lower than that after mutation of CAC in the second motif to GCG (RD6m4 vs RD6m5 in Table 1), while mutation of AGC in the first motif or AGC in the second motif to CTG had a similar effect on PhoP binding (RD6m6 vs RD6m7).
The first motif discovered (motif P1) is most similar to the GCN4-like motif (GLM).
For each pair of motifs (including TATAAA), the upstream regions were divided into four categories: Upstream regions that contained the first motif but not the second, upstream regions that contained the second motif but not the first, upstream regions that contained neither of the two motifs, and upstream regions that contained both motifs (the intersection).
Finally, the second motif AYNxG is also conserved while the Ala residue is often replaced by a Ser.
