©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (1): 537-551 (2013) In silico comparative analysis and expression profle of antioxidant proteins in plants S. Sheoran 1 , B. Pandey 1 , P. Sharma 1 , S. Narwal 2 , R. Singh 1 , I. Sharma 4 and R. Chatrath 3 1 Plant Biotechnology, Directorate of Wheat Research, Karnal, India 2 Quality and Basic Sciences, Directorate of Wheat Research, Karnal, India 3 Crop Improvement, Directorate of Wheat Research, Karnal, India 4 Project Director, Directorate of Wheat Research, Karnal, India Corresponding author: S. Sheoran E-mail: sheoran_sonia@yahoo.co.in Genet. Mol. Res. 12 (1): 537-551 (2013) Received March 5, 2012 Accepted October 7, 2012 Published February 27, 2013 DOI http://dx.doi.org/10.4238/2013.February.27.3 ABSTRACT. The antioxidant system in plants is a very important defensive mechanism to overcome stress conditions. We examined the expression profle of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) using a bioinformatics approach. We explored secondary structure prediction and made detailed studies of signature pattern of antioxidant proteins in four plant species (Triticum aestivum, Arabidopsis thaliana, Oryza sativa, and Brassica juncea). Fingerprinting analysis was done with ScanProsite, which includes a large collection of biologically meaningful signatures. Multiple sequence alignment of antioxidant proteins of the different plant species revealed a conserved secondary structure region, indicating homology at the sequence and structural levels. The secondary structure prediction showed that these proteins have maximum tendency for α helical structure. The sequence level similarities were also analyzed with a phylogenetic tree using neighbor- joining method. In the antioxidant enzymes SOD, CAT and APX, three major families of signature were predominant and common; these were PKC_PHOSPHO_SITE, CK2_PHOSPHO_SITE and N-myristoylation