Bioinformatics analysis of the oxidosqualene cyclase gene and the amino acid sequence in mangrove plants

International Conference on Computing and Applied Informatics 2016

物理学;计算机科学

Basyuni, M.^1 ; Wati, R.^1

Department of Forestry, Faculty of Forestry, University of Sumatera Utara, J1. Tri Dharma Ujung No. 1, Medan, North Sumatera

20155, Indonesia^1

关键词: Amino acid sequence;    Bioinformatics analysis;    Bioinformatics methods;    Oxidosqualene cyclases;    Phylogenetic trees;    Physical and chemical properties;    Secondary structures;    Subcellular localizations;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/801/1/012011/pdf
DOI  :  10.1088/1742-6596/801/1/012011

学科分类：计算机科学（综合）

来源: IOP

【 摘 要 】

This study described the bioinformatics methods to analyze seven oxidosqualene cyclase (OSC) genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, similarity, subcellular localization and phylogenetic. The physical and chemical properties of seven mangrove OSC showed variation among the genes. The percentage of the secondary structure of seven mangrove OSC genes followed the order of a helix > random coil > extended chain structure. The values of chloroplast or signal peptide were too low, indicated that no chloroplast transit peptide or signal peptide of secretion pathway in mangrove OSC genes. The target peptide value of mitochondria varied from 0.163 to 0.430, indicated it was possible to exist. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove OSC genes. To clarify the relationship among the mangrove OSC gene, a phylogenetic tree was constructed. The phylogenetic tree shows that there are three clusters, Kandelia KcMS join with Bruguiera BgLUS, Rhizophora RsM1 was close to Bruguiera BgbAS, and Rhizophora RcCAS join with Kandelia KcCAS. The present study, therefore, supported the previous results that plant OSC genes form distinct clusters in the tree.