In silico sequence analysis of predicted beta-amylase 7-like protein in Juglans regia L.

Emre Sevindik


Walnut (Juglans regia L.) is a deciduous tree of the Juglandaceae family. Beta-amylase (β-amylase, EC is an enzyme that catalyses hydrolysis of glycosidic bonds in polysaccharides. In this study; sequence, physicochemical, and three-dimensional analyses of predicted β-amylase 7-like protein in Juglans regia using various bioinformatic tools were conducted. The physicochemical properties of the predict β-amylase 7-like protein were analyzed by using ExPASy ProtParam tool that revealed the molecular weight (MW), Isoelectric Points (pI), total number of negatively charged residues (Asp + Glu), total number of positively charged residues (Arg + Lys), instability index, aliphatic index, and GRAVY (Grand Average of Hydropathy) values. Subcellular localization using CELLO v.2.5, putative phosphorylation sites using NetPhos 3.1 server, domain analysis using Pfam, and secondary structure prediction using SOPMA were accom-plished. To predict the 3D structure of the predict β-amylase 7-like protein, homology models were applied using PSIPRED, RAMPAGE, and PyMOL programs. The results of our study provide insight into fundamental characteristics of the predicted β-amylase 7-like protein in Juglans regia.


Juglans regia; β-amylase 7-like; In silico

Full Text:



Wani MS, Hussain A, Ganie SA, Munshi AH, Lal EP, Gupta RC. Juglans regia. A revıew. Int J Latest Res Sci Technol. 2016; 5(1): 90-97.

Pereira JA, Oliveira I, Sousa A, Ferreira ICFR, Bento A, Estevinho L. Bioactive properties and chemical composition of six walnut (Juglans regia L.) cultivars. Food Chem Toxicol. 2008; 46: 2103-2111.

Oliveira I, Sousa A, Ferreira ICFR, Bento A, Estevinho L, Pereira JA. Total phenols, antioxidant potential and antimicrobial acivity of walnut (Juglans regia L.) green husky. Food Chemical Toxicol. 2008; 46: 2326-2331.

Fernández-Agullóa A, Pereirab E, Freirea MS, Valentãoc P, Andradec PB, González-Álvareza J, Pereirab JA. Influence of solvent on the antioxidant and antimicrobial properties of walnut (Juglans regia L.) green husk extracts. Indust Crops Prod. 2013; 42: 126-132.

Sun M, Wang Y, Song Z, Fang G. Insecticidal activities and active components of the alcohol extract from green peel of Juglans mandshurica. J For Res. 2007; 18: 62-64.

Yiğit D, Yiğit N, Aktaş E, Özgen U. Antimicrobial activity of walnut (Juglans regia L.). Turk Microbiol Soc. 2009; 39(1-2): 7-11.

Filiz E, Koç İ. In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L. J. BioSci Biotech. 2014; 3(1): 61-67.

Doehlert DC, Duke SH, Anderson L. Beta-amylases from alfalfa (Medicago sativa L.) roots. Plant Physiol. 1982; 69: 1096-1102.

Liu HL, Chen WJ, Chou SN. Mechanisms of aggregation of alpha- and beta-amylases in aqueous dispersions. Colloids Surfaces B: Biointerfaces. 2003; 28: 215-225.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013; 30: 2725-2729.

Idrees S, Nadeem S, Kanwal S, Ehsan B, Yousaf A, Nadeem S, Rajoka MI. In silico sequence analysis, homology modeling and function annotation of Ocimum basilicum hypothetical protein G1CT28_OCIBA. Int J Bioautomat. 2012; 16(2): 111-118.

Wilson DB. Cellulases and biofuels. Curr Opin Biotechnol. 2009; 20(3): 295-299.

Vuong Thu V, David B Wilson. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng. 2010; 107(2): 195-205.

Podell S, Gribskov M. Predicting N-terminal myristoylation sites in plant proteins. BMC Genomics. 2004; 5: 37.

Klimczak LJ, Collinge MA, Farini D, Giuliano G, Walker JC, Cashmore AR. Reconstitution of Arabidopsis casein kinase II from recombinant subunits and phosphorylation of transcription factor GBF1. Plant Cell. 1995; 7(1): 105-115.

Zhang S, Jin CD, Roux SJ. Casein kinase II-type protein kinase from pea cytoplasm and its inactivation by alkaline phosphatase in vitro. Plant Physiol. 1993; 103(3): 955-962.

Koenig M, Grabe N. Highly specific prediction of phosphorylation sites in proteins. Bioinformatics. 2004; 20(18): 3620-3627.

Colovos VC, Yeates TO. Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci. 1993; 2: 1511-1519.


  • There are currently no refbacks.