KinG: a database of protein kinases in genomes

Abstract

The KinG database is a comprehensive collection of serine/threonine/tyrosine-specific kinases and their homologues identified in various completed genomes using sequence and profile search methods. The database hosted at http://hodgkin. mbu.iisc.ernet.in/ approximately king provides the amino acid sequences, functional domain assignments and classification of gene products containing protein kinase domains. A search tool enabling the retrieval of protein kinases with specified subfamily and domain combinations is one of the key features of the resource. Identification of a kinase catalytic domain in the user's query sequence is possible using another search tool. The occurrence and location of critical catalytic residues if the query has a catalytic kinase domain, recognition of non-kinase domains in the sequence and subfamily classification of the kinase in the query will help in deciphering the biological role of the kinase. This online compilation can also be used to compare the protein kinases of a given subfamily and domain combinations across various genomes. Another exclusive feature of the database is the collection of the Ser/Thr/Tyr protein kinases and similar sequences encoded in the genomes of archaea and bacteria.

Figure 1

Domain diversity of representative protein kinases belonging to various subfamilies of protein kinases extracted from the KinG database. Protein kinase domains are shown in red. (a) Domain combination of protein kinases with the RGS domains characteristic of the AGC_4 subfamily of protein kinases, involved in desensitization of G-protein-coupled receptors. PH, pleckstrin homology domain. Protein kinase representatives from this family are found in H.sapiens, D.melanogaster and C.elegans. Homologues of this subfamily of kinases are not found in S.cerevisiae. (b) Protein kinases with domains known to be involved in ubiquitination. UBA, ubiquitin-associated domain; Usp, universal stress protein domain; U-box, modified ring finger domain found in proteins involved in ubiquitination. UBA-domain-containing protein kinases are found in the CAMK, AGC and PTK subfamilies of A.thaliana, H.sapiens and D.melanogaster. Protein kinases containing ubiquitin domains encoded in H.sapiens and D.melanogaster belong to the CAMK subfamily. Arabidopsis thaliana in addition encodes another class of ubiquitin-related protein kinases with a U-box, which belong to the plant receptor kinase subfamily.