Bio::DB::Align::ProtClustDB has a similar interface with Bio::DB::Align::Pfam, which support retrieving alignment file from Prosite.
get_Aln_by_id #retrieve the alignment using ID, and returns a Bio::SimpleAlign object
get_Aln_by_acc #retrieve the alignment using accession, and returns a Bio::SimpleAlign object
id2acc #conversion of id to accession
acc2id #conversion of accession to id