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OJBTM

Online Journal of Bioinformatics

 

Volume 8 (2):177-187, 2007.


Structure and function prediction of a hypothetical protein (Q307B9_SPIPL) of Spirulina platensis (Nordstedt) Geitler.

 

Lakshmi PTV 1, Uma Maheswari S1, Annamalai A2

 

1Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore-46, Tamil Nadu, India. 2 School of Dietetics and Human Nutrition, McGill University, Macdonald Campus, Montreal, Quebec, Canada

 

ABSTRACT

 

Lakshmi PTV, Uma Maheswari S, Annamalai A, Structure and Function Prediction of a Hypothetical Protein (Q307B9_SPIPL) of Spirulina platensis (Nordstedt) Geitler, Online Journal of Bioinformatics, 8 (2) : 177-187, 2007. Using homology modeling, a high quality of protein 3D structure has been predicted for the hypothetical amino acid sequence Q307B9_SPIPL of Spirulina platensis and was also compared to the abinitio predicted structure through ROSETTA. However, the quality of the homology model performed through SWISS-MODEL depended on the quality of the sequence alignment by BLAST and template structure. A comparative assessment of secondary structure modeled using GOR IV, HNN and SOPMA revealed greater percentage of residues as alpha helix and random coils against the beta sheets. Validation of the tertiary structure by PROCHECK revealed that the structure modeled through SWISS-MODEL to be of high quality with 90.8% of residues in the most favored region. Structure comparison by VAST for the ROSETTA modeled structure indicated no hits for the entire sequence unlike that of  SWISS modeled structure, which indicated 60 structure neighbors for the entire residues. Moreover, function prediction through SCANPROSITE and PFAM identified a pattern PS00142 encoding Zinc Protease and three other domains - DUF 45 (domain of unknown function), Semialdehyde dehydrogenase and Herpes UL92 domain; while the same through INTERPROSCAN identified only two signatures (IPR002725 and IPR006025) referring to  DUF 45 and  Zinc binding site respectively.

 

Key words: Homology Modeling, Hypothetical Protein, Spirulina platensis, Structure Comparison, Procheck Validation, Function Prediction, Signatures, Zinc protease, Domain of Unknown Function.


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