Informatics Publishing Limited

Swapnil Ganesh Sanmukh ¹, Waman Narayan Paunikar ¹

Affiliations
1 Applied Aquatic Ecosystem Division, National Environmental Engineering Research Institute, Nehru Marg, Nagpur-440020, IN

Abstract

The Shigella phages are the bacterial viruses infecting various Shigella species. Their role in conversion of non-pathogenic Shigella strains to pathogenic are well studied, hence there is a need to understand the genetic makeup imparting such characteristics to their host. The present paper is an attempt to understand some of the known Shigella phages by studing their hypothetical proteins. The complete genome sequence of 3 Shigella phages viz, Shigella phage Sf6, Shigella phage phiSboM-AG1and Shigella phage SP16 revealed the presence of various hypothetical proteins. The probable function prediction of the 275 hypothetical proteins amongs the three phages was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM, COGs and CATH. However, structure prediction for only 21 hypothetical proteins was possible by using PS2 protein modeling server. This study revealed the presences of functional domain in hypothetical proteins of Shigella phages; their roles are yet to be discovered. These interpreted data for hypothetical proteins can be used for the understanding of functional, structural, evolutionary and metabolic development of Shigella phages and its life cycle along with their role in host evolution.

Keywords

Bacterial Viruses, Genetic Makeup, Bioinformatics Web Tools, Conserved Domains, Life Cycle, Host Evolution.

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Swapnil Ganesh Sanmukh ¹, Waman Narayan Paunikar ¹

Affiliations
1 Ecosystem Division, National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur-440020, Maharashtra, IN

Abstract

The Human herpes Viruses are the potential agents for causing watery blisters in the skin or mucous membranes of the mouth, lips or genitals. The complete genome sequences for various known Human herpes viruses have been done which deciphered the presence of various gene sequences for unknown proteins. We analyzed complete genome of 10 such viruses from which 3 were selected for our studies. Our attempt is to predict the structure and function of these proteins by the application of computational methods. The probable function prediction of the protein is done by using bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching sequence databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. While tertiary structures were constructed using PS2 Server (Protein Structure Prediction server). These studies revealed presences of enzymatic functional domain in 6 proteins; their roles are yet to be discovered in Human herpes Viruses. These data can be used for the understanding of evolutionary development of Human herpes Viruses and its life cycle during host pathogenicity.

Keywords

Unknown Proteins, Bioinformatics Web Tools, Conserved Domains, Functional Domain, Life Cycle, Host Pathogenicity.

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Waman Narayan Paunikar ¹, Swapnil Ganesh Sanmukh ¹, Tarun Kanti Ghosh ¹

Affiliations
1 Applied Aquatic Ecosystem Division, National Environmental Engineering Research Institute, Nehru Marg, Nagpur-440020, IN

Abstract

The Rhizophages are the viruses that infect the Rhizobium spp. present in soil and ischolar_main nodule of nitrogen fixing bacteria. The genome sequencing of some Rhizophages highlights the presence of various gene sequences for hypothetical proteins which are still unclassified. We analyzed complete genome of 3 Rhizophages for hypothetical proteins for our studies. This attempt is made to predict the structure and function of these hypothetical proteins by the application of computational methods. The probable function prediction of the hypothetical protein was done by using bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching orthologous conserved domains in the hypothetical sequences. While tertiary structures were constructed using PS2 Server (Protein Structure Prediction server). The 105 uncharacterized proteins were functionally classified and structures were predicted for 39 hypothetical protein. This information of hypothetical proteins can be used for the understanding of structural, functional and evolutionary development of Rhizophages and Rhizobium spp.

Keywords

Nitrogen Fixing Bacteria, Bioinformatics Web Tools, Conserved Domains, Uncharacterized Proteins, Evolutionary Development.

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