Prediction of Target Substrates of Transporters in Escherichia coli

Transporters play an important role in maintaining the cellular homeostasis by uptaking ions or nutrients and by effluxing metabolic end products, wastes or toxins. These membrane proteins constitute one of the largest protein families in prokaryotes and eukaryotes and are responsible for various physiological functions. Consequently, if one transporter can’t transport its specific substrate, the cell will be disordered. On the other hand, if the drug transporter is overexpressed, antibiotics will permeate membrane easily, result in drug resistance. Prediction of substrates of transporters are important for assigning functions in molecular level to hypothetical genes and for planning to further experimental design for determining their function. To attain this, we have developed prediction method of substrates of transporters based on amino acid sequence. In concrete terms, we have systemized and predicted function of transporter comprehensively using phylogenetic analysis and Hidden Markov Model based on a multiple alignment of the transporter protein sequences, and also using Evolutionary Trace method for predicting amino acid residues involved in substrate specificity.