Protein Sequences MSA vs. BLASTp

Hello everyone here! I am recently working on ligand discovery. What I’m doing now is to find out if the ligand which targets the pathogen’s specific enzyme will also have effect on human’s.

I do BLAST to pathogen’s protein to look for similar proteins in human. The identity and similarity given by BLAST are different from the MSA one(I use clustal omega). I wonder which algorithm is better to fit my work.

I am new to bioinformatics, and thank you for your patience.