PhosphoBase is a database of experimentally verified phosphorylation sites and associated protein kinases. The data are collected from literature and the SwissProt database and stored in a relational SQL database. Version 3.0 contains 1766 phosphorylated residues with 1310 protein kinase annotations. PhosphoBase is available on the World Wide Web from the CBS Server at http://www.cbs.dtu.dk/databases/PhosphoBase
1. Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ. (2004) Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5:79
2. Diella F, Gould CM, Chica C, Via A, Gibson TJ. (2007) Phospho.ELM: a database of phosphorylation sites update 2008. Nucleic Acids Res. Epub Oct 25, 2007
The database of BActerial Nucleoside MOnophosphate KInases (BANMOKI) is a collection of homology-based models of three-dimensional structures of all five bacterial nucleoside monophosphate kinases (NMPK) families, their pre-computed properties and other relevant information. Each entry in the database contains the following information sequence identity, PDB file of 3D model structure, Enzyme Commission (EC) number, pKa values of all titratable groups, desolvation penalty, interaction energy with permanent dipoles and the net charge of folded and unfolded states as a function of pH. We also have implemented a search engine using combination of CGI Perl programs and embedded Java scripts. User can search either within the whole database or within the particular family with respect of any combination of the following parameters: name, sequence ID, values of pKa and its components. An option to download all or part of the search results is also available. Users are given a choice of searching for values exactly equal to (with 5% tolerance level), larger than, smaller than or between desired value(s). The search results can then be sorted in ascending or descending order by any of searchable parameters. Users can also choose either AND or OR conjunction between the search criteria.
Recent develoments :
The database is currently being updated to include the new sequences and to take advantage of the new available templates and is currently upgraded to include the models of the post reaction (holo) form of all family members.
The web server development and the corresponding scientific work was supported by NATO collaborative grant CBP.EAP.CLG 981749.
As one database with two functionally different web interfaces, PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data. PlantsP focuses on proteins involved in the phosphorylation process (i.e. kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins. Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains. Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. PlantsP is available at http://plantsp.sdsc.edu and PlantsT is available at http://plantst.sdsc.edu.
Recent develoments :
The original PlantsP database has been extended to include PlantsT as a second view based on a common data and software model. A proteotyp system for acquiring and peer-reviewing user annotation has been implemented and is in use with over 200 registered users.
This work is supported by the funding from National Science Foundation Plant Genome Program, DBI-9975808 (PlantsP) and DBI- 0077378 (PlantsT). This work is also assisted by the facilities of the National Biomedical Computation Resource at SDSC (NIH P41-RR08605).
1. Gribskov M, Fana F, Harper J, Hope DA, Harmon AC, Smith DW, Tax FE, Zhang G. (2001) PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res. Jan 1;29(1):111-3.
2. Van Belle D, Andre B. (2001) A genomic view of yeast membrane transporters. Curr Opin Cell Biol. Aug;13(4):389-98. Review.
3. Ward JM. (2001) Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics. Jun;17(6):560-3.
4. Krysan,P.J., Young,J.K. and Sussman,M.R. (1999). T-DNA as an Insertional Mutagen in Arabidopsis. Plant Cell, 2, 2283?2290.
5. Saier, M.H. (1999) A functional-phylogenetic system for the classification of transport proteins. J Cell Biochem.;Suppl 32-33:84-94. Review.
6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. Sep 1;25(17):3389-402. Review.
7. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. Dec 15;25(24):4876-82.
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.
Recent develoments :
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