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Title

Homology modeling and assigned functional annotation of an uncharacterized antitoxin protein from Streptomyces xinghaiensis

 

Authors

Arafat Rahman Oany1*, Md Shahabuddin Ahmed1, Nasreen Jahan1, Md Abdul Latif 1, Shahin Mahmud1, Md. Ahmed Hossain1, Fatema Akter 2, Hasibul Haque Rakib1, Md. Shariful Islam1

 

 

Affiliation

1Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh; 2Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.

 

Email

arafatr@outlook.com ; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received November 01, 2015; Accepted November 04, 2015; Published November 30, 2015

 

Abstract

Streptomyces xinghaiensis is a Gram-positive, aerobic and non-motile bacterium. The bacterial genome is known. Therefore, it is of interest to study the uncharacterized proteins in the genome. An uncharacterized protein (gi|518540893|86 residues) in the genome was selected for a comprehensive computational sequence-structure-function analysis using available data and tools. Sub-cellular localization of the targeted protein with conserved residues and assigned secondary structures is documented. Sequence homology search against the protein data bank (PDB) and non-redundant GenBank proteins using BLASTp showed different homologous proteins with known antitoxin function. A homology model of the target protein was developed using a known template (PDB ID: 3CTO:A) with 62% sequence similarity in HHpred after assessment using programs PROCHECK and QMEAN6. The predicted active site using CASTp is analyzed for assigned anti-toxin function. This information finds specific utility in annotating the said uncharacterized protein in the bacterial genome.

 

Keywords

antitoxin, homology modeling, active-site residues, prediction, hypothetical protein, Streptomyces xinghaiensis

 

Citation

Oany et al. Bioinformation 11(11):493-500 (2015)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.