Magnetospirillum magneticum (AMB-1), which belong to alpha-protobacterium are gram-negative, single-celled prokaryotic organisms consisting of a lash-like cellular appendage called flagella. These filamentous structures are made up of a protein called flagellin that in turn consist of four sub-domains, two inner domains (D0, D1) made up of alpha-helices and two outer domains (D2, D3) made up of beta sheets. It is wrapped in a helical fashion around the longitudinal filament with the outermost sub-domain (D3) exposed to the surrounding environment. This study focuses on the interaction of the D3 with semiconducting as well as metallic single-walled carbon nanotubes (m-SWNT) and in turn presents the interactive forces between the SWNT and D3 from the perspective of size and type of SWNT. It is found that the SWNT interacts the most with glycine and threonine residues of flagellin both electrostatically as well as through van der waals. Further, the viability of magnetotactic bacteria Magnetospirillum magneticum (AMB-1) in the presence of SWNT is experimentally investigated and it is found that magnetotaxis in AMB-1 is preserved without any toxic effects due to SWNT. It is proposed that AMB-1 can be used as an efficient carrier of carbon nanotubes through its flagellum for semiconductor nanofabrication tasks.