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

Abstract

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. Subcellular 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 Background: Streptomyces are soil-conquering gram-positive bacteria and a member of the order of Actinomycetales [1]. Streptomyces xinghaiensis, a novel species of Streptomyces, was isolated from a marine sediment sample collected from Xinghai Bay, Dalian, China [2]. The S. xinghaiensis draft genome contains 7,618,725 bp with a GC content of 72.5%, representing approximately 92.7% of the 8.2-Mb estimated size of the genome. Analysis of the genome revealed a number of genes related to the biosynthesis of secondary metabolites. At least 15 clusters involved in secondary metabolism were identified; these include one gene cluster that highly resembles the gene cluster of ribostamycin [3], an amino-glycoside antibiotic. Toxinantitoxin (TA) system was widely adopted in many genomes like bacteria and archaea and is usually recognized as a maintenance or stability mediator [4, 5]. Although, the exact role of this system in the genome is not clear but, acts as sentinels against DNA loss and various stress managemen