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. Scientific literature is also a source for identifying related sequences, especially very diverged members that might be missed in a single sequence search. The more sequences the better. Multiple alignments of two and three sequences have limited usefulness. If you think your sequences form sub-groups than try to also separately align these.
Redundant sequences are separate sequences that are highly similar to each other.
The extreme example is a set of identical sequences. Obviously only one sequence of the set should be used, the rest do not contribute to finding the alignment. Worse, the redundant sequences will bias the al ignment toward their own features. Ideally all sequences in the aligned group should have a comparable similarity to each other. This threshold could be modified for different cases and the results evaluated.