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OJBTM
Online
Journal of Bioinformatics ©
Volume 14 (2): 226-234, 2013
Virtual
analysis of catalytic site in Plasmodium yoelii yoelii
Akash
Kumar
Department of Bioinformatics
, Uttaranchal College of
Science & Technology, Dehradun, India,
ABSTRACT
Kumar
A., Virtual analysis of catalytic site in Plasmodium yoelii
yoelii, Onl
J Bioinform., 14 (2):
226-234, 2013. Protein
sequence of Plasmodium
yoelii yoelii
“prt_seq No definition line
found “ was extracted from GenPept
database (ACCESSION EAA21357) and used to
predict hydrophobicity,
atomic and amino
acid composition, PEST region, solvent accessibility,
molecular mass,
theoretical pI and its
catalytic site in 3D. The PEST
region suggested an intracellular half-life <2hr. The
molecule was composed
of 1395 carbon, 2254 hydrogen, 462 oxygen, 386 nitrogen and
7 sulfur atoms. Aspargine
concentration was 13.9% and the N-terminal was Methionine. Total number of
negatively charged residues
was 44 and positive 42 with total atoms 4504. Secondary
structure composition
was determined with Hidden Markov model, and disulphide
bonds, effect of point
mutation prediction and catalytic site identification with HeatMap. Online active site
prediction was determined
by matching protein sequences with a library of catalytic
sites yielding 26
regions with a maximum score of 0.015 for Orotidine “
5'-monophosphate decarboxylase” and a minimum of 0.004 for
“Endo-alpha-sialidase”. The
molecular weight of the protein sequence
was 32049.9 and Theoretical Pi value 6.08.
Protein close to given Pi and molecular mass was
matched using TagIdent yielding
126466 proteins. The Instability Index
was 36.19 and stable. The aliphatic Index occupied alanine,
valine,
isoleucine, and leucine was
80.77. The three
dimensional structure of catalytic site was visualized using
Jmol software.
Keywords: Catalytic site, Heatmap
representation, Propsearch,
Solvent accessibility, PEST
region.