NAR Molecular Biology Database Collection entry number 518

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

Rakshambikai, R.,Tyagi, N., Garnier, N., Dinesh, D. C., 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

Database of Kinases in Genomes (KinG) 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://king.mbu.iisc.ernet.in/ which provides detailed listing of the Ser/Thr/Tyr and atypical protein kinases in various organisms, accompanied by other features such as protein kinase subfamily classification and domain organization. A part of KinG is the database of human kinase splice variants. List of 918 human protein kinases encoded by 445 genes is provided with details of subfamily classification and domain architecture. In the current version of king, 20 new species, Fusarium Wilt, Honey Bee, Leishmania, Pinkrot Agent, Seedling Agent, Spikemoss, Wheat Fungi, Blood Fluke, Gb Fungus, Brown Rust, Gibberella, Perigord, Plb Agent, Sea Anemone,Whb Fungus, Placozoan, Purple Urchin, Smut Fungus, Water_Flea have been added and one Nectria has been updated. The database also enables the retrieval of protein kinases belonging to specified subfamily or with specific domain combination. User-specified protein sequences can be queried against the database for identifying the protein kinase catalytic domain and various functional residues in the catalytic kinase domain.

(a) Multiple profiles for the various families under different groups of Protein kinases have been added for both Prokaryotes and Eukaryotes. These may be downloaded and used for classifying sequences into various Hanks and Hunter groups using RPS-BLAST [2] search.(b) Classification of prokaryotic kinases [3] has been provided. This part of the database contains information about details of specific clusters of prokaryotic kinase sequences at the taxonomic level, Multiple sequence alignment file of clusters, Distance matrices, domain organization and the amino acid sequences for catalytic domain region. (c) Hanks and Hunter group classification [4] has been adopted to classify kinases from Fusarium oxysporum, Apis mellifera, Leishmania major, Phytophthora sojae, Pythium ultimum, Selaginella moellendorffii, Mycosphaerella graminicola, Schistosoma mansoni, Phaeosphaeria_nodorum, Puccinia triticina, Gibberella moniliformis, Tuber melanosporum, Phytophthora infestans, Nematostella vectensis, Gibberella zeae, Trichoplax adhaerens, Strongylocentrotus purpuratus, Ustilago maydis, Daphnia pulex, Nectria haematococca. (d) KinG v2.0 website has been improved and provides a new look. Predictions of protein kinases for various completely sequenced genomes are added constantly and the current release (v2.0) of the KinG database has been updated by considering various completely sequenced eukaryotic and prokaryotic genomes. The updated version of KinG holds information for 512 organisms. In the current version, kinome information is available for 49 archaea, 259 eubacteria, 126 viruses and 78 eukaryotes. 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. Recently, KinG v2.0 is the only on-line database which provides information on the kinome complement of various eukaryotic, viral and prokaryotic genomes with splice variants information on human kinases [6].

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. Gowri VS,Tina KG,Krishnadev O,Srinivasan N. Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. Proteins 2007; 67: 789–794. 3.Tyagi N, Anamika K, Srinivasan N, 2010 A Framework for Classification of Prokaryotic Protein Kinases. PLoS ONE 5(5): e10608. doi:10.1371/journal.pone.0010608 4.Hanks SK, Hunter T: Protein kinases 3. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. Faseb J 1995, 9(8):576-596. 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 6. Anamika, K., Garnier, N., Srinivasan, N. (2009) Functional diversity of human protein kinase splice variants marks significant expansion of human kinome. BMC Genomics., 10:622.

Go to the abstract in the NAR 2004 Database Issue.

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