Sequence alignment is an important tool for identifying regions of similarities among proteins and for, thus, establishing functional and structural relationships between different proteins. Here, alignments of transmembrane domains (TMDs) of viral channel forming proteins with host ion channels and toxins are evaluated. The following representatives of polytopic viral channel proteins are chosen: (i) p7 of HCV and 2B of Polio virus (two TMDs) and (ii) 3a of SARS-CoV (three TMDs). Using ClustalW2, each of the TMDs of the viral channels is aligned, and the overlap is mapped onto structural models of the host channels and toxins focusing on the pore-lining TMDs. The analysis reveals that p7 and 2B TMDs align with the pore-facing TMD of MscL, and 3a-TMDs align with those of ligand-gated ion channels. Possible implications concerning the mechanism of function of the viral proteins are discussed.