NAR Molecular Biology Database Collection entry number 518

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

Anamika, K., Martin, J., Krupa, A, Abhinandan, K.R., and 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, virus, 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 with other features such as protein kinase subfamily classification and domain organisation. The updated KinG provides links to UniProt, NCBI and Pfam 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 function al residues in the catalytic kinase domain. If the query is identified to have a kinase domain additional information on the domain organisation and the domain architecture are also provided. Full length sequence of protein kinases for every organism can also be retrieved.

Prediction for protein kinase for various completely sequenced genomes are added constantly and the current release (1.5) of the KinG database has been updated using the latest release of Pfam (version 22), which comprises of 9318 protein families. The updated version of KinG holds information on over 17457 protein kinases encoded in the genomes of 374 organisms. In the current version, 235 additional organisms which include eukaryotes, viruses and prokaryotes, have been included. In the current release of KinG, 35 eukaryotic genomes, 149 eubacterial genomes, 32 archaeal genomes and 19 viral genomes have been added which is making a total of 54 eukaryotic genomes, 275 eubacterial genomes and 49 archaeal genomes. In the current update, we have introduced and analysed 16 fungal, 5 algal and 19 viral kinomes. For the identification and subfamily classification of putative protein kinases in the updated version of KinG, multiple position specific scoring matrices (MulPSSM) approach [2] has been used. The domain organisation of all the protein kinases has been defined according to the recent Pfam release. The updated kinome analyses for various protozoa like Plasmodium species, Entamoeba histolytica, Trychomonas vaginalis, Trypanosoma species [3-5] are also listed in the current release. Various pathogenic fungal kinome and viral kinome dataset can also be retrieved from the current release. Apart from these informations, kinome data for the two completely sequenced fish genomes Danio rerio and Tetraodon nigroviridis and five algal genomes, have also been provided. To our knowledge, KinG is the only one on-line database which provides information on kinome complement of various eukaryotic, viral and prokaryotic genomes. With the exponential rise in the number of completely sequenced genomes, the updated version of KinG is hoped to shed light on signal transduction pathways of various organisms and hope to be a useful resource for comparison of repertoires of protein kinases in closely related and divergent species.

This research is supported by 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. 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
3. Anamika, K., Srinivasan, N. (2007) Comparative kinomics of Plasmodium organisms: unity in diversity. Protein Pept Lett., 14: 509-517
4. Anamika, K., B hattacharya, A., Srinivasan, N. Analysis of the protein kinome of Entamoeba histolytica. Proteins (In press)
5. Parsons, M., Worthey, E. A., Ward, P., N., Mottram, J. C. (2005) Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics, 6:127.

Go to the abstract in the NAR 2004 Database Issue.

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