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OJBTM
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,
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.