Final answer:
The "pilot protein" involved in the transfer of DNA into a recipient cell during a DNA packaging process similar to conjugation is called VirD2. It covalently links to the 5'-end of the transferred DNA and is comparable to bacterial conjugation mechanisms in E. coli involving the F pilus.
Step-by-step explanation:
The protein that is referred to as the "pilot protein" because it covalently links to the 5'-end of the transferred DNA and leads the DNA into the recipient cell during the DNA packaging process is the VirD2 protein. This process is part of a mechanism employed by Agrobacterium tumefaciens to insert a segment of its DNA into plant host cells, a process similar to bacterial conjugation.
In bacterial conjugation, a conjugation pilus, such as the F pilus in E. coli, facilitates direct DNA transfer from one prokaryote to another. DNA transfer and packaging involve the action of various enzymes; among them, DNA ligase plays a vital role by catalyzing the formation of covalent phosphodiester linkages between DNA fragments, important in both eukaryotic and prokaryotic genetic material processing.