This paper presents novel reconfigurable semi-systolic array architecture for the Smith-Waterman with an affine gap penalty algorithm to align protein sequences optimized for shorter database sequences. This architecture has been modified to enable hardware reuse rather than replicating processing elements of the semi-systolic array in multiple FPGAs. The proposed hardware architecture and the previously published conventional one are described at the Register Transfer Level (RTL) using VHDL language and implemented using the FPGA technology. The results show that the proposed design has significant higher normalized speedup (up to 125%) over the conventional one for query sequence lengths less than 512 residues. According to the UniProtKB/TrEMBL protein database (release 2015_05) statistics, the largest number of sequences (about 80%) have sequence length less than 512 residues that makes the proposed design outperforms the conventional one in terms of speed and area in this sequence lengths range.