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Sequence and Structure Comparison Studies of Phycocyanin in Spirulina Platensis

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Author(s): Lakshmi P.T.V. | Uma Maheswari S. | Karthikeyan P.P. | Annamalai A.

Journal: Journal of Computer Science & Systems Biology
ISSN 0974-7230

Volume: 01;
Issue: 01;
Start page: 063;
Date: 2008;
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Keywords: Spirulina platensis | Phycocyanin | BLAST | Phylogeny | VAST | Structural Neighbors

ABSTRACT
Crystal structure of Spirulina platensis for Phycocyanin with PDB ID 1GH0 was revealed to contain 24 chains named from 1GH0A to 1GH0X. It was observed that the alternate chains consisted of same sequence however, the odd chains (1GH0A, 1GH0C, 1GH0E… 1GH0W) and even chains (1GH0B, 1GH0D, 1GH0F… 1GH0X) contained 162 and 172 amino acid residues respectively in a similar pattern. Sequence comparison revealed 100 BLAST hits and phylogenetic tree was traced for alternate chains. Similarity percentages of hits were calculatedfor 1GH0A chain was revealed to have 84 % hits of cyanobacterial sequences, 12 % hits of rhodophyta sequences, and 4% hits of eugliphida, cyanophora and artificial vector sequences respectively. Similarity percentages of hits were calculated for 1GH0B chain was revealed to have 73 % hits of cyanobacterial sequences, 20%hits of rhodophyta sequences, and 5% hits of cryptophyta sequences, and 1% hits of eugliphida and 1% hits of cyanophora sequences respectively. Structure comparisons of these sequences examined by VAST showed residues of alternate entire chains from 1 to 162 and from 1 to 172 residues to contain 1323 structure neighbors.1628 structure neighbors were found for the phycobilisome domain family which is the major accessory light-1628 harvesting complexes of cyanobacteria and red algae.
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