PROMALS3D (PRofile Multiple Alignments with Predicted Local Structures and 3D constraints) takes into account the sequence identity, secondary structure and 3D arrangement in predicting similarities between related proteins. 1PROMALS3D was particularly helpful(for me) in designing primers to insert certain protein sequences in creating a chimera motor construct.
One can find the protein sequences of interest from NCBI, or from other sequencing programs that would translate the cDNA into amino acid sequences. Once sequences are obtained, one can copy and paste the sequences into the PROMALS3D website, preceding with >seq(insert name here). An example is shown below.
By inputing the structural information, one can reduce 'incorrect' alignment of protein sequences that may have structural homology, but not necessarily sequence homology. Once the related structural information is obtained from the Protein Data Bank(PDB ), ID codes corresponding to the sequences can be added (in order). The PDB includes x ray crystallographic data that has been published by other scientists all around the world. This angstrom-scale resolution provides lots of structural information that would otherwise be lost or not accounted for in a normal protein sequence alignment.