Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach

Lactobacillus acidophilus bacteria are widely used as probiotic and to produce various healthy fermented food products. The PNW3 strain of the bacteria has numerous proteins in its genome and some are considered as hypothetical proteins. The aim of the present study was to predict the structures and biological functions of the hypothetical protein (accession number: TDB29877.1) from L. acidophilus through an in-silico approach applying various bioinformatics tools. The sequence similarity was searched on the available biological databases using BLASTp program to find out the homologues proteins. Besides, determination of various properties like physicochemical characteristics, subcellular localization, phylogenetic analysis, functional annotation, protein-protein interaction, determination of secondary and tertiary structures, active site detection and further quality assessment analysis were done using appropriate computational methods of bioinformatics. In-silico analysis revealed that the hypothetical protein has contained TerB-N and TerB-C domains with the presence of YjbR-like superfamily. The Protein-protein interaction network analysis revealed that the protein highly interacted with various known and unknown proteins responsible for iron ion binding, DNA and RNA metabolisms and numerous repair mechanisms that maintain cellular integrity. It was also found that the protein has predominantly alpha-helices in its secondary structure and the three dimensional model has been found to be novel as it possessed expected quality while gone through various quality assessment tools. Thus, the present result indicated that the selected hypothetical protein which is cytoplasmic in nature with Belta-grasp fold, plays important role in responding during stress condition or phage defense mechanism.