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OJBTM
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.
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