Identification of Protein Motifs in Phytoplasma Associated with Root (Wilt) Disease of Coconut (Cocos nucifera) Using an Improved Statistical Measure

Abstract

Protein motif is a conserved short region within larger sequence, and it provides an important way to get functional or structural information about a noble protein sequence. This study primarily provides a new approach to identify motifs which are considered to play an important role to determine functional or structural class of any protein. Coconut palm (Cocos nucifera L.) root (wilt) disease (CRWD) became a serious concern for coconut cultivation in the coastal region of South India. It has already been reported that species of the phytoplasma (-belonging to ribosomal group 16SrXI) is primarily associated with CRWD. In this study, our objective is to modify an existing motif identification algorithm, and also identify motifs that describe their conserved region within a CRWD phytoplasma protein sequence. Accordingly, the existing information content measure formulas for a no-gapped and gapped aligned sequence set were re-formulated. Further, an improvement on both these existing measures has been vied by incorporating prior information of BLOSUM90 substitution matrix. Results showed that proposed modifications could successfully identify N-terminal myristoylation motif within an alignment matrix of Arabidopsis thaliana sequences; concurrently our modification has also been validated. Both the approaches, namely frequency- and BLOSUM90-based information content, have been compared using the observed results, in terms of identified motifs. Finally, we could also test this noble BLOSUM90-based approach to correctly predict conserved regions at locations, (163–171) and (117–138), in an aligned secA gene sequence set of phytoplasma, an etiological agent of CRWD.