It is better to go from the simple to the complex. For example, before trying to identify new family members by querying a database with a multiple alignment of the family one should try straight-forward database searches with the single sequences. The results from the single sequence searches can provide more sequences to the alignment together with confirming the multiple alignment and the results of searches made with it. Protein sequences can be related by homology or convergence. In both cases multiple alignment can be attempted.
Homologous proteins have a common ancestor and typically a common function.
Converged proteins independently evolve to have common sequence features that typically preform a common function or have a common structure. Do not confuse the terms homology and similarity . Sequences either have or not have a common ancestor. Proteins that have significant sequence similarity are most often homologous. Frequently we only have a single protein sequence.