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OJBTM
Online Journal
of Bioinformatics©
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.