Location of substrate-determining residues in protein kinase A using HMM alignment. The profile HMM S_TKc from the SMART database was aligned to rat PKA (UniProt accession P27791) using the HMMER program hmmsearch. The 6 motifs used to locate SDRs are shown in bold. SDRs are underlined. The KE loop, used to determine the SDRs for the substrate +2 position is italicised. SDRs used in substrate prediction for Ser/Thr-kinases are summarised under the alignment. Position refers to the number of residues N- or C-terminal to the substrate phosphorylation site. SDRs that determine the +2 position depend on KE loop length as follows: length 12–17 = AMK+10, AMK+11, AMK+12; length 18–20 = AMK+12, AMK+13, AMK+14; length < 12 or > 20 = E-7, E-6, E-5.