PMC

Construction of substrate scoring matrices using SQL queries to the PredikinDB database. Schematic showing how sequence features from a query protein kinase are used to query PredikinDB and generate Predikin scoring matrices.

Design and construction of the PredikinDB database. (a) Illustration showing how a UniProt entry is parsed to link protein kinase sequences (names in bold) with phosphorylation sites. (b) PredikinDB table schema showing links between fields. Field headers in italics are primary keys. Abbreviations in parentheses indicate the UniProt line from which the field was derived. For clarity, 38 fields containing key protein kinase residues used in substrate prediction are summarised as one field.

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.