Applying kinesin-microtubule (MT) system in vitro as gliding assay provides great possibility of manipulating materials at nanometer scales. Gliding directions of MTs is controlled by electrical field and charges of cargoes. Integrating these techniques, autonomous molecular separation system corresponding to the difference between charges of cargoes is expected to be designed. In order to evaluate the influence of charges of cargoes on gliding trajectories of MTs quantitatively, therefore, we measured electrophoretic mobility of cargo-attached MTs. From this measurement, we estimated gliding trajectories of MTs and evaluated these by calculating curvatures.