Perhaps you have a set of annotated antibody sequences and you want to align them all by their annotations i.e. all CDR residues, vh, vl etc. aligned to each other (as opposed to aligning by sequence or structure similarity). This can be accomplished using the Sequence | Alignment | Align Residue Identifiers command (see attached screenshot below).

When executing this command on an active Sequence Window it adds gaps to all visible sequences to align residues with matching residue identifiers including insertion code. Hidden sequences are not aligned. Chain view domains and fixed blocks are maintained.