The protein model of somatic embryogenesis genes of oil palm (Elaeis guineensis Jacq.) using Phyre2 and Swiss-model

• Published in: IOP conference series. Earth and environmental science 2024-05, Vol.1352 (1), p.012042
• Main Authors: Astari, R P, Basyuni, M, Siregar, L A M, Damanik, R I M, Arifiyanto, D, Syahputra, I
• Format: Article
• Language: English
• Subjects: Amino acids; Cell culture; Confidence intervals; Embryonic growth stage; Genes; Helices; Oil palm trees; Proteins; Similarity; Somatic embryogenesis; Vegetable oils
• ISSN: 1755-1307; 1755-1315
• DOI: 10.1088/1755-1315/1352/1/012042

Somatic embryogenesis (SEs) is the capacity of plant-generated embryo structures to form a somatic cell. SEs in oil palm is one of the techniques used to produce clones with superior characteristics. It can maximize the oil palm crop’s productivity, whose demand increases every year. The identification of the structure of proteins can optimize the efficiency of the selection of the embryogenic culture. The somatic embryogenesis genes were collected from GeneBank at the NCBI. This study successfully describes the protein modeling of tree somatic embryogenesis genes in oil palms by Phyre2 and the Swiss model software. The ENOD93, HOX1 and RIk-OPff with the varied protein prediction the protein model of ENOD93 was detected with confidence of 81.5% by Phyre2, sequence identity of 76.6% with a range of 3-96 amino acids, and sequence similarity of 0.63 by Swiss-model. The sequence similarity of HOX1 was detected at 100% with a confidence level of 99.7% by the Swiss model. The protein model of RIk-OPff was predicted with 100% confidence in the range of 30–536 amino acids, and only in these genes were the trans-membrane helices.