[2] Protein kinase catalytic domain sequence database: Identification of conserved features of primary structure and classification of family members

Publisher Summary To help cope with the rapidly expanding protein kinase family, a database of the catalytic domain amino acid sequences has been established. This database would be a useful resource for the initial classification of novel protein kinases and for other studies that require extensive sequence comparisons. The catalytic domain database is updated frequently and often includes new sequences before they can be found in the Genbank/EMBL/PIR resources. More importantly, the availability of this large group of sequences in a single file saves investigators from the tedious task of collecting them themselves. This chapter describes the current makeup of the catalytic domain database and present two examples of its use: analysis and graphic display of conserved catalytic domain residues using conservation plots and classification of protein kinases by phylogenetic mapping. A prerequisite for both of these tasks is a multiple sequence alignment. The protein kinase catalytic domain database file can be obtained electronically over Internet using the standard network file transfer program (FTP). The database file PKINASES.IG contains brief descriptions of the kinases and references for the sequences. One hundred and seventeen distinct sequences had been entered by mid-February, 1990. Seventy-five of these are taken from protein-serine/threonine kinases and 42 from protein-tyrosine kinases. Sixty-eight of the sequences are from vertebrate species, 24 from yeasts (both budding and fission), 18 from Drosophila, two from nematode, and one each from Aplysia, Aspergillus, Hydra, bean plant (Phaseolus), and avian erythroblastosis virus S13. 43 of the 68 current vertebrate entries are taken from human sources and twenty two of the remaining vertebrate sequences derive from four other mammals: bovine, rabbit, rat, and mouse.