The Corynebacterium glutamicum ATCC 13032 prophage CGP3 encodes an actin-like protein, AlpC that was shown to be involved in viral DNA transport and efficient viral DNA replication. AlpC binds to an adapter, AlpA that in turn binds to specific DNA sequences, termed alpS sites. Thus, the AlpAC system is similar to the known plasmid segregation system ParMRS. So far it is unclear how the AlpACS system mediates DNA transport and, whether AlpA and AlpC functionally interact. We show here that AlpA modulates AlpC filamentation dynamics in a dual way. Unbound AlpA stimulates AlpC filament disassembly, while AlpA bound to alpS sites allows for AlpC filament formation. Based on these results we propose a simple search and capture model that explains DNA segregation by viral AlpACS DNA segregation system.