It is better to proceed 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 straightforward database searches with the single sequences. The results from the single sequence searches can provide more sequences to the alignment and confirm the multiple alignment and 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 motifs that typically perform a common function. Frequently we only have a single protein sequence. Querying sequence databases with the sequence we have can identify other members. The search should be repeated with every found member until no more sequences are found. A keyword search of the database can be done when only the protein name is known and when we wish to verify that all sequences were found.