BMC Genomics 2009, 10:622 http://www.biomedcentral.com/1471-2164/10/622 Results and discussion Identification and analysis of a comprehensive collection of human protein kinases Currently, there are two online sites that constantly update the information on repertoire of human protein kinases gleaned periodically from the releases of human genome data. These data sets KinG [Kinases in Genome http://hodgkin.mbu.iisc.ernet.in/~king] [32] and kinase.com http://kinase.com/kinbase/FastaFiles/ are quite similar in terms of list of human kinases and their classification into subfamilies. Both these datasets of human kinome are obtained as a result of careful use of highly sophisticated sequence analysis tools. For example, in the recent releases of KinG database http://hodg kin.mbu.iisc.ernet.in/~king, we have employed highly sensitive multiple profile search approach [33,34]. During this update of the database and analysis many protein kinases have come into light which are splice variants of previously identified protein kinases listed in various kinome datasets such as the one in http://www.itb.cnr.it/ kinweb[11]. This prompted us to extend and analyse the repertoire of protein kinase gene products by including protein kinase splice variants in the dataset. The improved human genome data enriched with information on splice variants available in ENSEMBL database http:// www.ensembl.org/Homo_sapiens/index.html has helped us to analyze protein kinase splice variants which were not studied in the previous genome-wide studies on kinases using the draft version of human genomic data [2-4]. In the current analysis, using various sensitive profile search methods (discussed in Materials and Methods sec- tion), we report 918 putative human protein kinase gene products (Additional file 1). In addition this list inte- grated with user-friendly search options is also available as a part of KinG database at http://hodg kin.mbu.iisc.ernet.in/king/cgi/search. All these 918 kinase gene products have catalytic aspartate, which acts as catalytic base, suggesting that these gene products are likely to possess phosphotransferase activity. Sequences lacking the catalytic aspartate (protein kinase-like non- kinases) have not been included in the current list. There are 445 genes which are encoding 918 protein kinase products. There are 209 genes which are encoding only one protein kinase. Remaining 236 kinase genes give rise to more than one gene product which are splice variants. Maximum number of splice variants generated from a protein kinase gene is 12. We checked for the expression of the human protein kinase splice variants using the publicly available cDNA data ftp://ftp.ensembl.org/pub/current_fasta/ homo_sapiens/cdna/ and found that 894 out of 918 have known cDNA data. Hence overwhelming majority of the recognized protein kinase genes is probably expressed and represents functional proteins. We have compared our kinome data set to kinase.com http://www.kinase.com in which so far 516 protein kinase gene products have been listed of which 25 are atypical protein kinases which are different from typical eukaryotic protein kinase super- family discussed in the current analysis. Classification of protein kinase gene products These putative protein kinases have been further classified into various subfamilies as proposed by Hanks and Hunter [35]. The most represented protein subfamily in human is CAMK (Ca2+/Calmodulin dependent Protein Kinase) (Additional file 1 and http://hodg kin.mbu.iisc.ernet.in/king/cgi/search) group of protein kinases regulated by Calcium/Calmodulin having 161 members which is followed by CMGC (CDK, MAPK, GSK3, CK2) group of protein kinases which have 149 members. There are 130 protein products belonging to AGC group of kinases which are mainly second messenger regulated kinases. Several members which are closely related to protein tyrosine kinase family and Tyrosine kinase-like (TKL) subfamily have also been identified. TKL family is quite diverse which have members (e.g. Raf, Mixed-lineage kinase, Activin and beta-receptor kinase, Interleukin 1 receptor associated kinase etc.) resembling both tyrosine and Serine/Threonine kinase families. Human kinases splice variants with potentially diverse functions: revealed from sequence analysis Interestingly there are examples of newly recognized splice variants encoded by a single gene which differ markedly in length and have different domain organiza- tion. Such prominent differences indicate that these splice variants might have different mode of regulation and dif- ferent functional properties. Additional File 2 represents set of such protein kinase splice variants which have dif- ferent domain organisation. For example while two pro- tein kinases (ENSP00000300843 and ENSP00000262893) with their catalytic domains closely resembling MARK subfamily has UBA (Ubiquitin-associ- ated domain) domain following the kinase domain; how- ever a splice variant (ENSP00000262891) has an extra domain, KA1 (Kinase-associated domain), apart from kinase and UBA domains (Figure 1A). KA1 domain teth- ered to protein kinase catalytic domain indicates a role of this kinase in ubiquitin pathway. Similarly, regulatory domain CAMII_AD domain which has role in multimeri- zation is usually found tethered to the Calcium/Calmod- ulin dependent protein kinase II (CAMKII). CAMII_AD domain is absent in one of the splice variants which has a kinase domain closely related to CAMKII subfamily (ENSP00000369096) while this regulatory domain is present in three splice variants (ENSP00000339740, ENSP00000378032, ENSP00000378034) (Figure 1B). In the same way, one of the four splice variants Page 3 of 7 (page number not for citation purposes)