Mycolyl-transferases are a family of proteins that are specifically present in the CMN (Corynebacterium, Mycobacterium and Nocardia) genera and are responsible for the synthesis of cell wall components. We modeled the three-dimensional structures of mycolyl-transfersases from Corynebacterium and Nocardia using homology modeling methods based on the crystal structures of mycolyl-transferases from M. tuberculosis. Comparison of the models revealed significant differences in their substrate binding site. Some mycolyl-transferases identified by the following Gene Ids: Nfa25110, Nfa45560, Nfa7210, Nfa38260, Nfa32420, Nfa23770, Nfa43800, Nfa30260, Dip0365, Ncgl0987, Ce1488, Ncgl0885, Ce0984, Ncgl2101, Ncgl0336, Ce0356 are associated with a relatively larger substrate binding site and amino acid residue mutations (D40N, R43D/G, S236N/A) are likely to affect binding to trehalose.