I would like to know how you align the amino acid sequences from different databases?For example, if I wish to know about cytoplasmic domains of TLR's.
I am not aware of how to generate the information from data sources.
For aligning anything you should grab the sequences from database and make a cumulative sequence file in FASTA format. For proteins, I would go for uniprot where we get curated protein sequences. Collect the sequences you are interested in and submit it to any available online (clustal W etc..) MSA tool and have fun.