The half reactions of ω-aminotransferase (ω-AT) from Vibrio fluvialis JS17 (ω-ATVf) were carried out using purified pyridoxal 5′-phosphate-enzyme (PLP-Enz) and pyridoxamine 5′-phosphate-enzyme (PMP-Enz) complexes to investigate the relative activities of substrates. In the reaction generating PMP-Enz from PLP-Enz using L-alanine as an amine donor, L-alanine showed about 70% of the initial reaction rate of (S)-α-methylbenzylamine ((S)-α-MBA). However, in the subsequent half reaction recycling PLP-Enz from PMP-Enz using acetophenone as an amine acceptor, acetophenone showed nearly negligible reactivity compared to pyruvate. These results indicate that the main bottleneck in the asymmetric synthesis of (S)-α-MBA lies not in the amination of PLP by alanine, but in the amination of acetophenone by PMP-Enz, where conformational restraints of the enzyme structure is likely to be the main reason for limiting the amine group transfer from PMP-Enz to acetophenone. Based upon those half reaction experiments using the two amino acceptors of different activity, it appears that the relative activities of the two amine donors and the two acceptors involved in the ω-AT reactions can roughly determine the asymmetric synthesis yield of the target chiral amine compound. Predicted conversion yields of several target chiral amines were calculated and compared with the experimental conversion yields. Approximately, a positive linear correlation (Pearson's correlation coefficient = 0.92) was observed between the calculated values and the experimental conversion yields. To overcome the low (S)-α-MBA productivity of ω-ATVf caused by the possible disadvantageous structural constraints for acetophenone, new ω-ATs showing higher affinity to benzene ring of acetophenone than ω-ATVf were computationally screened using comparative modeling and protein-ligand docking. ω-ATs from Streptomyces avermitilis MA-4680 (SAV2612) and Agrobacterium tumefaciens str. C58 (Atu4761) were selected, and the two screened ω-ATs showed higher asymmetric synthesis reaction rate of (S)-α-MBA and lower (S)-α-MBA degradation reaction rate than ω-ATVf. To verify the higher conversion yield of the variants of ω-ATs, the reaction with 50 mM acetophenone and 50 mM alanine was performed with coupling of lactate dehydrogenase and two-phase reaction system. SAV2612 and Atu4761 showed 70% and 59% enhanced yield in the synthesis of (S)-α-MBA compared to that of ω-ATVf, respectively. Biotechnol. Bioeng. 2011;108: 253–263. © 2010 Wiley Periodicals, Inc.