Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates
pLogos for Protein Kinase A (A, B), Casein Kinase II (C, D), and control (E, F) illustrate preferred residues by position. Note, pLogos are derived from phosphorylation sites in E. coli obtained using the ProPeL methodology (after subtraction of endogenous phosphorylation sites). In each pLogo, residue heights are proportional to their log binomial probabilities in the context of the E. coli background with residues above the x-axis indicating overrepresentation and residues below the x-axis indicating underrepresentation. The central residue in each pLogo is fixed and denotes the modification site. The pLogos and corresponding extracted motifs (see Figure 2) are highly consistent with the known basophilic specificity of PKA and acidophilic specificity of CK II. Additionally, the control phosphorylation sites (i.e., endogenous E. coli phosphorylation sites) do not conform to a motif and lack any statistically significant residues.