The quark mixing matrix $V_{CKM}$ is studied in depth on the basis of superstring inspired $SU(6)times SU(2)_R$ model with global flavor symmetries. The sizable mixings between right-handed down-type quark $D^c$ and colored Higgs field $g^c$ potentially occur but no such mixings in up-type quark sector. In the model the hierarchical pattern of $V_{CKM}$ is understood systematically. It is shown that due to large $D^c$-$g^c$ mixings $V_{ub}$ is naturally suppressed compared to $V_{td}$. It is pointed out that the observed suppression of $V_{ub}$ is in favor of the presence of $SU(2)_R$ gauge symmetry but not in accord with generic SU(5) GUT.