In this work we study spectra of $^7$Be, $^7$Li, $^8$Be and elastic scattering cross sections $^4$He($^3$He, $^3$He)$^4$He, $^4$He($^3$H, $^3$H)$^4$He within the Gamow shell model (GSM) in the coupled-channel formulation (GSM-CC). The evolution of channel amplitudes and the alignment of the many-body state with the decay channel in the vicinity of the channel threshold is studied for selected states. The GSM-CC in multi-mass partition formulation applied to a translationally invariant Hamiltonian with an effective finite-range two-body interaction reproduce well the spectra of $^7$Be, $^7$Li, $^8$Be and elastic scattering reactions: $^4$He($^3$He, $^3$He)$^4$He, $^4$He($^3$H, $^3$H)$^4$He. Detailed analysis of the dependence of reaction channel amplitudes on the distance from the particle decay threshold allowed to demonstrate the alignment of the wave function in the vicinity of the decay threshold. This analysis also demonstrates the appearance of clustering in the GSM-CC wave function in the vicinity of the cluster decay threshold. We demonstrated that GSM formulated in the basis of reaction channels including both cluster and proton/neutron channels allows to describe both the spectra of nuclei with low-energy cluster thresholds and the low-energy elastic scattering reactions with proton, $^3$H, and $^3$He projectiles. Studying dependence of the reaction channel amplitude in a many-body state on distance from the threshold, we showed an evolution of the $^3$He, $^4$He clustering with increasing separation energy from the cluster decay threshold and demonstrated a mechanism of the alignment of many-body wave function with the decay threshold, i.e. the microscopic reorganization of the wave function in the vicinity of the cluster decay threshold which leads to the appearance of clustering in this state.