Systematic search for putative new domain families in Mycoplasma gallisepticum genome

We have developed a new method for the identification of domains in unassigned regions through indirect connections and scaled up its application to the analysis of 434 unassigned regions in 726 protein sequences of Mycoplasma gallisepticum genome. We could establish 71 new domain relationships and probable 63 putative new domain families through intermediate sequences in the unassigned regions, which importantly represent an overall 10% increase in PfamA domain annotation over the direct assignment in this genome.The systematic analysis of the unassigned regions in the Mycoplasma gallisepticum genome has provided some insight into the possible new domain relationships and putative new domain families. Further investigation of these predicted new domains may prove beneficial in improving the existing domain prediction algorithms.Domain assignment to the protein sequences has paramount importance in the post genomic era. Protein domains are the structural, functional and evolutionary units of proteins. Study of proteins at the domain level has had a profound impact on the study of individual proteins. Experimental and/or computational methods can be used to identify domains in the given protein sequence. Classification databases such as the Dali Domain Dictionary[1], CATH[2], SCOP[3] and DIAL[4] employ structural data to locate and assign domains. Identification of domains at the sequence level depends on the detection of global and local sequence similarities between a given query sequence and domain sequences found in databases such as Pfam[5]. Due to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. The realization of additional domains in those circumstances can be tedious, involving manual intervention, but can lead to better understanding of overall biological function. We have recently introduced an automatic multi-step approach, PURE for recognizing such connections[6,7].Mycopl