NAR Molecular Biology Database Collection entry number 518

http://hodgkin.mbu.iisc.ernet.in/~king

Anamika, K., Tyagi, N., Martin, J., Krupa, A, Abhinandan, K.R., Srinivasan, N.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India

Contact ns@mbu.iisc.ernet.in

The KinG database is an on-line compilation of the putative Ser/Thr/Tyr kinases encoded in the completely sequenced genomes of prokaryotes, viruses and eukaryotes (1). The full complement of protein kinases in various completely sequenced genomes is hosted at http://hodgkin.mbu.iisc.ernet.in/~king which provides detailed listing of the Ser/Thr/Tyr and atypical protein kinases in various eukaryotic, viral and prokaryotic organisms, accompanied by other features such as protein kinase subfamily classification and domain organisation. The updated KinG provides links to UNIPROT (2), the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov.in) and Pfam (3) domain families for the proteins listed. The database also enables the retrieval of protein kinases belonging to specified subfamily or with specific domain combination. User-specified protein sequences can be analysed for the presence of the protein kinase catalytic domain and various functional residues in the catalytic kinase domain. Additional information on domain organisation and architecture are also provided. Full length sequence of protein kinases for every organism can also be retrieved.

Predictions of protein kinases for various completely sequenced genomes are added constantly and the current release (1.6) of the KinG database has been updated by considering various completely sequenced eukaryotic and prokaryotic genomes. The updated version of KinG holds information for 483 organisms. In the current version, kinome information is available for 49 archaea, 254 eubacteria, 126 viruses and 54 eukaryotes. In the current update, we have introduced the chimpanzee (Pan troglodytes) kinome and the kinomes of 125 viral genomes. In the current version, the human kinome has been freshly analysed using the refined human genomic data from the latest release of Ensembl (4). For the identification and subfamily classification of putative protein kinases in the updated version of KinG, a multiple position-specific scoring matrices approach (5) has been used. To our knowledge, KinG is the only on-line database which provides information on the kinome complement of various eukaryotic, viral and prokaryotic genomes. In addtion, KinG also provides information on the non-kinase domains which are tethered to the kinase domain. With the exponential rise in the number of completely sequenced genomes, the updated version of KinG is expected to shed light on the signal transduction pathways of various organisms and to be a useful resource for the comparison of repertoires of protein kinases in closely related and divergent species.

This research is supported by the Department of Biotechnology, Government of India, New Delhi to N.S.

1. Krupa, A., Abhinandan, K.R., Srinivasan N. (2004) KinG: a database of protein kinases in genomes. Nucleic Acids Res. 32: D153-D155
2. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33: D154-159.
3. Bateman, A., Birney, E., Cerruti, L., Durbin R., Etwiller L., Eddy, S.R., Griffiths-Jones,S., Howe K.L., Marshall, M., Sonnhammer, E.L. (2002). The Pfam protein families database. Nucleic Acids Res, 30: 276-280
4. Hubbard, T.J., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S.C., Fitzgerald, S., Fernandez-Banet, J., Graf, S., Haider, S., Hammond, M., Herrero, J., Holland, R., Howe, K., Howe, K., Johnson, N., Kahari, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Melsopp, C., Megy, K., Meidl, P., Ouverdin, B., Parker, A., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Severin, J., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wood, M., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X.M., Flicek, P., Kasprzyk, A., Proctor, G., Searle, S., Smith, J., Ureta-Vidal, A., Birney, E. (2007) Ensembl 2007. Nucleic Acids Res. 35 D610-D617
5. Gowri, V.S., Krishnadev, O., Swamy, C.S., Srinivasan, N. (2006) MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. Nucleic Acids Res., 34: D243-6

Go to the abstract in the NAR 2004 Database Issue.

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