Data Mining and Knowledge Engineering

Swapnil G. Sanmukh ¹, Waman N. Paunikar ¹

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

Abstract

The Yersinia species are responsible for plague disease. These host bacteria are infected by their specific phages. The association of phage-host and their genetic interaction within the living bacterial cell are imparting various beneficial characteristics to its host helping it for retaining suitable characteristics for adaptation as well as evolution. The understanding of Yersinia phages can help us to know how they influence their host functional characteristics. The Yersinia phages can be understood by analyzing their hypothetical protein sequences within its genome. Our study included 102 hypothetical proteins from 6 different Yersinia phage genomes. The function predictions in 48 hypothetical proteins and 3-D structures were predicted for 5 protein sequences using PS2 server. The probable function prediction was 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. This study identified many proteins, whose roles are yet to be discovered in Yersinia phage or their bacterium. These results can be used for understanding the role of Yersinia phages in co-evolution of their hosts.

Keywords

Plague, Genetic Interactions, Hypothetical Proteins, Bioinformatics Web Tools, Co-Evolution.

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Swapnil G. Sanmukh ¹, Waman N. Paunikar ¹, Dilip B. Meshram ¹, Tarun K. Ghosh ¹

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

Abstract

The Vibrio parahaemolyticus is the potential food poisoning agent. The complete genome sequencing of Vibrio parahaemolyticus has been done which deciphered the presence of various gene for hypothetical proteins whose function is not yet understood. We analyzed complete genome of Vibrio parahaemolyticus for hypothetical proteins from which 458 were functionally classified into their respective protein families. Our attempt is to predict the functions of these hypothetical proteins by the application of computational methods and Bioinformatics. The probable function prediction of the hypothetical protein was 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. These study revealed presences of enzymatic functional domain in 458 uncharacterized proteins; their roles are yet to be discovered in Vibrio parahaemolyticus. These deciphered enzymatic data for hypothetical proteins can be used for the understanding of functional, structural, evolutionary and metabolic development of Vibrio parahaemolyticus and its life cycle along with their role in host evolution and pathogenicity.

Keywords

Bioinformatics Web Tools, Conserved Domains, Uncharacterized Proteins, Life Cycle, Host Evolution.

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Swapnil G. Sanmukh ¹, Waman N. Paunikar ¹, Tarun K. Ghosh ¹

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

Abstract

Mycobacterium leprae Br4923 the causative agent of leprosy is one of the most puzzling and complex microorganism due to its gene decaying property and presence of large number of pseudogenes. The proper treatment of leprosy is not yet possible due to its drug resistance mechanism and uncultivable nature on culture media. The present work deals with the prediction of structure and function of hypothetical proteins in M. Leprae by the use of computational methods and bioinformatics. The prediction of orthologous sequence in biological sequence databases, assist in classification of 180 hypothetical protein sequences in their respective protein family by the use of web tools (CDD-BLAST, INTERPROSCAN, PFAM and COGs). The 3-D structures of the 160 functionally resolved hypothetical proteins were constructed using PS2 server (Protein structure prediction server). The generated data can prove useful in the prediction of evolutionary relationship of Mycobacterium leprae with those of other related Mycobacterium species. It may also assist in the designing of novel drug to treat leprosy.

Keywords

Gene Decay, Pseudogenes, Uncultivable, Web Tools, Evolutionary Relationship.

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