Evaluation of Lipid Transfer Protein (Ltp) 1 Gene in Sesame and Other Plants Using Bioinformatics Approach

Abstract

Abstract This study was aimed at using bioinformatics tools to characterize the Lipid Transfer Protein 1 gene in some selected accessions with special reference to Benny seed (Sesamum indicum) Lipid Transfer Protein 1 sequence as a query sequence. Nucleotide and amino acid sequences of 30 accessions were retrieved from NCBI database and analyzed for homology, physicochemical properties, motifs, GC content as well as phylogenetic relationships. Results showed that nucleotide and amino acid sequence lengths of this gene among the selected accessions differs. Its nucleotide length varied between 599–8461bp, while the amino acids sequence varied between 96–355 residues, Molecular weight range from 10008.77–35532.61daltons. With Sesamum indicum having the lowest molecular weight and Physcomitrium patens having the highest molecular weight. Result on the Theoretical PI was above 4.61 for all the amino acid sequences of Lipid Transfer Protein 1 gene in the selected accessions. It was observed that the total number of negatively charged residues ranged from 1–20. The instability index and aliphatic index ranged from 20.23–69.39, 73.48–102.24 respectively. Some of the proteins are stable, while twelve were considered unstable following the results for instability index. Extinction coefficient was highest for Sesamum indicum (14480). Daucus carota subsp. Sativus (-0213) is the only accessions with a negative GRAVY. The motifs N-glycosylation site, Plant lipid transfer proteins signature, N-myristoylation site, Casein kinase II phosphorylation site, Protein kinase C phosphorylation site were the most common across the selected accessions. GC content analysis revealed that it ranged from ranged from 29.73–54.55%. Analysis of the secondary structure of the amino acid sequences of the Lipid Transfer Protein 1 gene showed that the region covered by random coil was the highest in the sequences compared to alpha helix and extended strand. Alpha helix ranges from 33.11–54.31%, the extended strands ranged from 9.17–15.13%, while the random coil ranges from 32.77–51.16% across the accessions. Following the results of the present study, it can be concluded that Lipid Transfer Protein 1 gene sequence of Sesamum indicum is closely related to Lipid Transfer Protein 1 gene in Brachypodium distachyon and distant to that in Glycine max, Vigna unguiculata, Capsicum annum.