A first-principles approach is presented for the thermoelectricity in molecular junctions formed by a single molecule contact. The study investigates the Seebeck coefficient considering the source-drain electrodes with distinct temperatures and chemical potentials in a three-terminal geometry junction. We compare the Seebeck coefficient in the amino-substituted and unsubstituted butanethiol junction and observe interesting thermoelectric properties in the amino-substituted junction. Due to the novel states around the Fermi levels introduced by the amino-substitution, the Seebeck coefficient could be easily modulated by using gate voltages and biases. When the temperature in one of the electrodes is fixed, the Seebeck coefficient varies significantly with the temperature in the other electrode, and such dependence could be modulated by varying the gate voltages. As the biases increase, richer features in the Seebeck coefficient are observed, which are closely related to the transmission functions in the vicinity of the left and right Fermi levels.