Informatics Publishing Limited

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 Mycobacteriophages are the bacteriophages infecting different Mycobacterium species in nature. The hypothetical proteins in 17 different Mycobacteriophages were structurally and functionally characterized by using computational tools like CDD-Blast, Interproscan, pfam, COGS and protein structure prediction server (PS2 server). Near about 2188 hypothetical proteins were screened for presence of functional domains and structural classification. The function predictions for 586 hypothetical proteins and structure predictions for 171 hypothetical proteins were possible by using these Bioinformatics web tools. These results can prove helpful for proper understanding of functional, evolutionary and metabolic development of Mycobacterium species.

Keywords

Mycobacterium Species, Hypothetical Proteins, Bioinformatics Web Tools, Evolutionary and Metabolic Development.

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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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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, Maharashtra, IN

Abstract

The present study of hypothetical proteins in Salmonella phages was carried out for predicting their structure and function relationship. Such applications for bacteriophages are not yet reported and there is a great need to understand the mechanism by which they impart the virulence, resistance and other novel characteristics to the host they infect. We are reporting the structure and functions of hypothetical proteins in Salmonella phages for understanding their role in Salmonella spp. The complete analysis of hypothetical proteins from 8 different Salmonella phage genomes were carried out by the using bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching 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 110 uncharacterized proteins and 3-D protein structure were predicted for 29 hypothetical proteins. These deciphered enzymatic data for hypothetical proteins can be used for the understanding of functional, structural, and evolutionary development of Salmonella phages and its life cycle along with their role in host evolution and pathogenicity.

Keywords

Virulence, Bioinformatics Web Tools, Conserved Domains, Uncharacterized Proteins, Life Cycle and Pathogenicity.

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

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

Abstract

The Ictalurus punctatus is fresh water fish and is commercially used for food and as a sport fish. The different hypothetical proteins in this fish give an insight for understanding its life cycle. We characterized structurally and functionally 116 hypothetical proteins from Ictalurus punctatus by using computational tools like CDD-Blast, Interproscan, pfam, COGS, superfamily 1.75 and protein structure prediction server (PS2 server). The function predictions for 80 hypothetical proteins and structure predictions for 52 hypothetical proteins were possible by using these Bioinformatics web tools. The deciphered data for hypothetical proteins can be used for the understanding of structural, functional, evolutionary and metabolic development of Ictalurus punctatus.

Keywords

Bioinformatics Web Tools, Conserved Domains, Hypothetical Proteins, Life Cycle.

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