Table 3

Proteins encoded by hallmark viral genes
Protein	Function	Virus groups	Homologs in cellular life forms	Comments	References

Jelly-roll capsid protein (JRC)	Main capsid subunit of icosahedral virions	Picornaviruses, comoviruses, carmoviruses, dsRNA phage, NCLDV, herpesviruses, adenoviruses, papovaviruses, parvoviruses, icosahedral DNA phages and archaeal viruses	Distinct jelly-roll domains are seen in eukaryotic nucleoplasmins and in protein-protein interaction domains of certain enzymes	Certain icosahedral viruses, such as ssRNA phages and alphaviruses, have unrelated capsid proteins. In poxviruses, the JRC is not a virion protein but forms intermediate structures during virion morphogenesis	[13–15, 53, 54, 109–111]
Superfamily 3 helicase (S3H)	Initiation and elongation of genome replication	Picornaviruses, comoviruses, eukaryotic RCR viruses, NCLDV, baculoviruses, some phages (e.g., P4), plasmids, particularly, archaeal ones	S3H is a distinct, deep-branching family of the AAA+ ATPase class	Characteristic fusion with primase in DNA viruses and plasmids	[16, 112]
Archaeo-eukaryotic DNA primase	Initiation of genome replication	NCLDV, herpesviruses, baculoviruses, some phages	All viral primases appear to form a clade within the archaeo-eukaryotic primase family	Characteristic fusion with S3H in most NCLDV, some phages, and archaeal plasmids	[18]
UL9-like superfamily 2 helicase	Initiation and elongation of genome replication	Herpesviruses, some NCLDV, some phages	Viral UL9-like helicases form a distinct branch in the vast superfamily of DNA and RNA helicases	Fusion with primase in asfarviruses, mimiviruses	[53]
Rolling-circle replication initiation endonuclease (RCRE)/origin-binding protein	Initiation of genome replication	Small eukaryotic DNA viruses (parvo-, gemini-, circo-, papova), phages, plasmids, and eukaryotic helitron transposons	No cellular RCRE or papovavirus-type origin-binding protein; however, these proteins have a derived form of the palm domain that is found in the majority of cellular DNA polymerases	Papovaviruses have an inactivated form of RCRE that functions as origin-binding protein	[17–20]
Packaging ATPase of the FtsK family	DNA packaging into the virion	NCLDV, adenoviruses, polydnaviruses, some phages (e.g., P9, M13), nematode transposons	A distinct clade in the FtsK/HerA superfamily of P-loop NTPases that includes DNA-pumping ATPases of bacteria and archaea		[113]
ATPase subunit of terminase	DNA packaging into the virion	Herpesviruses, tailed phages	The terminases comprise a derived family of P-loop NTPases that is distantly related to Superfamily I/II helicases and AAA+ ATPases		[109, 114]
RNA-dependent RNA polymerase (RdRp)/reverse transcriptase (RT)	Replication of RNA genomes	Positive-strand RNA viruses, dsRNA viruses, retroid viruses/elements, possibly, negative-strand RNA viruses	Another major group of palm domains that are distinct from those in DNA polymerases	The RdRps of dsRNA viruses are homologs of positive-strand RNA virus polymerases. The provenance of negative-strand RNA virus RdRp remains uncertain although sequence motif and, especially, structural analysis suggests their derivation from positive-strand RNA virus RdRps	[23–25, 28, 87, 115]

Abbreviations: NCLDV, Nucleo-Cytoplasmic Large DNA Viruses
Koonin et al. Biology Direct 2006 1:29 doi:10.1186/1745-6150-1-29