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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.
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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