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OJBTM
Online Journal of Bioinformatics ©
In silico characterization
of bacterial, fungal and plant polygalacturonase
protein sequences
Amit
Kumar Dubey (MSc), Sangeeta Yadav (Ph.D), Ritika Rajput1 (MSc),
Gautam Anand (MSc) and Dinesh Yadav*(PhD).
Department of Biotechnology, D.D.U Gorakhpur
University, Gorakhpur,1Mahila Mahavidyalaya,
Banaras Hindu University, Varanasi, Uttar Pradesh India., *Corresponding author: Australian Centre for Plant Functional Genomics, University of
Adelaide, Glen Osmond, South Australia 5064, Australia.
ABSTRACT
Dubey AK, Yadav S, Rajput R, Anand G, Yadav D., In silico
characterization of bacterial, fungal and plant polygalacturonases
protein sequences, Onl J Bioinform,
13(2):246-259, 2012. Protein sequences
of bacterial, fungal and plants polygalacturonases
(PGs) retrieved from databases were characterized In Silico for similarity of stretch, conserved motifs and closeness through
construction of phylogenetic trees.
Multiple sequence alignment of plant PGs sequences showed similar amino
acids in the region 313-356, 361-383 and 393-547. Highly conserved AA asparatic acid, glycine, alanine,
histidine, aspargine
and lysine at specific sites were analyzed for fungal and bacterial PGs. Three distinct clusters representing fungal, bacterial
and plant polygalacturonases appeared in the
phylogenetic tree suggesting a relatively high degree of conserved sequences
for the 3 groups. The functional domains observed in the motifs of fungal and
plant PG were Glyco_hydro_28 and PLN03003 superfamily respectively, whilst
bacterial PG has PGU1, Glyco_hydro_28, and PLN03030 superfamily domains.
Keywords: Pectinases, Polygalacturonases, In silico, Motif,
Domain, Glyco_hydro_28
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