©1996-2019. All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned, must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
Online Journal of Bioinformatics ©
Volume 14 (2): 118-125, 2013
Predicted structure of an unknown protein sequence from US patent 8211428
Akash kumar1, Mohd. Zakir Khawaja2, Ahsan ul haq Qureshi3
1Department of Bioinformatics, 2Department of Biotechnology, 1,2Uttaranchal College of Science & Technology, Dehradun, India 3CENT & Chemistry Department King Fahd University of Petroleum and minerals Dhahran, Saudi Arabia
Kumar A, Zakir Khawaja M, Ul Haq Qureshi A., Predicted structure of an unknown protein sequence from US patent 8211428A. Onl J Bioinform., 14 (2): 118-125, 2013. The protein sequence of an unknown organism (US Patent 8211428) from GenPept database (ACCESSION AFO13014) was predicted using 3D structure, molecular weight, theoretical pI, atomic composition, transmembrane segment prediction and domain identification. The retrieved sequence was used for homology modelling to identify the organism and its species. Atomic composition result revealed that the protein sequence consisted of C1222H1916N354O371S17 with a molecular weight of 28047.8 kdal and 260 residues suggesting that the atomic composition is involved in the synthesis of the protein sequence and an iteration in any atom could change the sequence and its structure. The instability index (II) was found to be 32.17 which classifies the protein as stable. The theoretical pH was estimated to be 7.52 with 3880 atoms which suggest that the protein sequence carries no net electrical charge. The protein domain of the submitted sequence was Trypsin with 120, 212,73 active sites with an E-value of 1.4e-74. 3D modelling with 3d jigsaw server revealed the structure analyzed with Rasmol with 228 groups with 1753 bonds, 3 Helices, 18 Strands and 32 Turns. Blastp showed that the unknown protein sequence has complete similarity with Homo Sapiens and probably belongs to that species.
Keywords: 3D modeling, BLASTP, E-Value, Query Coverage.