In silico predictions of phosphorylation and ubiquitination sites in the MtRDR1 sequence

In silico translation of the MtRDR1 cDNA sequence was carried out using the ExPASy Translate tool (http://web.expasy.org/translate/) from the Swiss Institute of Bioinformatics ExPASy Bioinformatics Resource Portal. Potential phosphorylation sites in the MtRDR1 protein sequence were predicted using NetPhos 2.0 software (www.cbs.dtu.dk/services/NetPhos/) [69]. NetPhos 2.0 generates a score in the range 0.000 to 1.000 to indicate the likelihood of a serine, threonine or tyrosine being a phosphorylation site, with residues with a score >0.500 being assigned as potential phosphorylation sites. UbPred software (http://omictools.com/ubiquitination-sites-category) was used to predict potential ubiquitination sites [70]. Residues with ubiquitination scores >0.62 are assigned as potential ubiquitination sites, with scores in the range 0.62–0.69 being low confidence predictions and those in the range 0.69–0.84 being high confidence predictions.