Table 1 VSFs and their distribution in the viral supergroup.

FSFs in boldface could be potential VSFs based on the criterion described in the text. FSFs were referenced by either SCOP ID or css. For example, the P-loop containing NTP hydrolase FSF is c.37.1, where “c” is the α/β class of secondary structure present in the protein domain, “37” is the fold, and “1” is the FSF.

SCOP IDSCOP cssVenn groupFSF descriptionDistribution
69070a.150.1VAnti-sigma factor AsiAdsDNA
55064d.58.27VTranslational regulator protein regAdsDNA
48493a.120.1VGene 59 helicase assembly proteindsDNA
89433b.127.1VBaseplate structural protein gp8dsDNA
69652d.199.1VDNA binding C-terminal domain of the transcription factor MotAdsDNA
56558d.182.1VBaseplate structural protein gp11dsDNA
49894b.28.1VBaculovirus p35 proteindsDNA
160957e.69.1VPoly(A) polymerase catalytic subunit–likedsDNA
51289b.85.5VTlp20, baculovirus telokin-like proteindsDNA
88648b.121.6VGroup I dsDNA virusesdsDNA
161240g.92.1VT-antigen–specific domain–likedsDNA
118208e.58.1VViral ssDNA binding proteindsDNA
54957d.58.8VViral DNA binding domaindsDNA
51332b.91.1VE2 regulatory, transactivation domaindsDNA
56548d.180.1VConserved core of transcriptional regulatory protein vp16dsDNA
90246h.1.24VHead morphogenesis protein gp7dsDNA
47724a.54.1VDomain of early E2A DNA binding protein, ADDBPdsDNA
57917g.51.1VZn binding domains of ADDBPdsDNA
49889b.27.1VSoluble secreted chemokine inhibitor, VCCIdsDNA
89428b.126.1VAdsorption protein p2dsDNA
82046b.116.1VViral chemokine binding protein m3dsDNA
158974b.170.1VWSSV envelope protein-likedsDNA
47852a.62.1VHepatitis B viral capsid (hbcag)dsDNA-RT
111379f.47.1VVP4 membrane interaction domaindsRNA
48345a.115.1VA virus capsid protein alpha-helical domaindsRNA
69908e.35.1VMembrane penetration protein mu1dsRNA
75347d.13.2VRotavirus NSP2 fragment, C-terminal domaindsRNA
69903e.34.1VNSP3 homodimerdsRNA
75574d.216.1VRotavirus NSP2 fragment, N-terminal domaindsRNA
58030h.1.13VRotavirus nonstructural proteinsdsRNA
49818b.19.1VViral protein domaindsRNA, minus-ssRNA, plus-ssRNA
88650b.121.7VSatellite virusesssDNA
48045a.84.1VScaffolding protein gpD of bacteriophage procapsidssDNA
50176b.37.1VN-terminal domains of the minor coat protein g3pssDNA
75404d.213.1VVSV matrix proteinMinus-ssRNA
118173d.293.1VPhosphoprotein M1, C-terminal domainMinus-ssRNA
69922f.12.1VHead and neck region of the ectodomain of NDV fusion glycoproteinMinus-ssRNA
101089a.8.5VPhosphoprotein XD domainMinus-ssRNA
58034h.1.14VMultimerization domain of the phosphoprotein from Sendai virusMinus-ssRNA
50012b.31.1VEV matrix proteinMinus-ssRNA
48145a.95.1VInfluenza virus matrix protein M1Minus-ssRNA
143021d.299.1VNs1 effector domain–likeMinus-ssRNA
161003e.75.1VFlu NP-likeMinus-ssRNA
160453d.361.1VPB2 C-terminal domain–likeMinus-ssRNA
101156a.30.3VNonstructural protein ns2, Nep, M1 binding domainMinus-ssRNA
160892d.378.1VPhosphoprotein oligomerization domain–likeMinus-ssRNA
56983f.10.1VViral glycoprotein, central and dimerization domainsPlus-ssRNA
101257a.190.1VFlavivirus capsid protein CPlus-ssRNA
103145d.255.1VTombusvirus P19 core protein, VP19Plus-ssRNA
89043a.178.1VSoluble domain of poliovirus core protein 3aPlus-ssRNA
110304b.148.1VCoronavirus RNA binding domainPlus-ssRNA
101816b.140.1VReplicase NSP9Plus-ssRNA
140367a.8.9VCoronavirus NSP7–likePlus-ssRNA
143076d.302.1VCoronavirus NSP8–likePlus-ssRNA
144246g.86.1VCoronavirus NSP10–likePlus-ssRNA
103068d.254.1VNucleocapsid protein dimerization domainPlus-ssRNA
117066b.1.24VAccessory protein X4 (ORF8, ORF7a)Plus-ssRNA
143587d.318.1VSARS receptor binding domain–likePlus-ssRNA
159936d.15.14VNSP3A-likePlus-ssRNA
160099d.346.1VSARS Nsp1–likePlus-ssRNA
140506a.30.8VFHV B2 protein–likePlus-ssRNA
144251g.87.1VViral leader polypeptide zinc fingerPlus-ssRNA
141666b.164.1VSARS ORF9b–likePlus-ssRNA
55671d.102.1VRegulatory factor NefssRNA-RT
56502d.172.1Vgp120 coressRNA-RT
57647g.34.1VHIV-1 VPU cytoplasmic domainssRNA-RT
49749b.121.2EVGroup II dsDNA viruses VPdsDNA
103417e.48.1EVMajor capsid protein VP5dsDNA
140713a.251.1EVPhage replication organizer domaindsDNA
161008e.76.1EVViral glycoprotein ectodomain–likedsDNA, minus-ssRNA
110132b.147.1EVBTV NS2-like ssRNA binding domaindsRNA
82856e.42.1EVL-A virus major coat proteindsRNA
140809a.260.1EVRhabdovirus nucleoprotein–likeMinus-ssRNA
101399a.206.1EVP40 nucleoproteinMinus-ssRNA
55405d.85.1EVRNA bacteriophage capsid proteinMinus-ssRNA
68918a.140.4BVRecombination endonuclease VII, C-terminal and dimerization domainsdsDNA
50017b.32.1BVgp9dsDNA
58046h.1.17BVFibritindsDNA
56826e.27.1BVUpper collar protein gp10 (connector protein)dsDNA
161234g.91.1BVE7 C-terminal domain–likedsDNA
140919a.263.1BVDNA terminal proteindsDNA
89064a.179.1BVReplisome organizer (g39p helicase loader/inhibitor protein)dsDNA
160570d.368.1BVYonK-likedsDNA
51327b.90.1BVHead binding domain of phage P22 tailspike proteindsDNA
141658b.163.1BVBacteriophage trimeric proteins domaindsDNA
64210d.186.1BVHead-to-tail joining protein W, gpWdsDNA
51274b.85.2BVHead decoration protein D (gpD, major capsid protein D)dsDNA
159865d.186.2BVXkdW-likedsDNA
101059a.159.3BVB-form DNA mimic OcrdsDNA
58091h.4.2BVClostridium neurotoxins, “coiled-coil” domaindsDNA
47681a.49.1BVC-terminal domain of B transposition proteindsDNA
58059h.2.1BVTetramerization domain of the Mnt repressordsDNA
54328d.15.5BVStaphylokinase/streptokinasedsDNA
64465d.196.1BVOuter capsid protein sigma 3dsRNA
57987h.1.4BVInovirus (filamentous phage) major coat proteinssDNA
160940e.66.1BEVApi92-likedsDNA
160459d.362.1BEVBLRF2-likedsDNA
109859a.214.1BEVNblA-likedsDNA
54334d.15.6BEVSuperantigen toxins, C-terminal domaindsDNA
51225b.83.1BEVFiber shaft of virus attachment proteinsdsDNA, dsRNA
49835b.21.1BEVVirus attachment protein globular domaindsDNA, dsRNA
50203b.40.2BEVBacterial enterotoxinsdsDNA, ssDNA
111474h.3.3BEVCoronavirus S2 glycoproteindsDNA, plus-ssRNA
56831e.28.1BEVReovirus inner layer core protein p3dsRNA
109801a.30.5AVHypothetical protein D-63dsDNA
161229g.90.1ABVE6 C-terminal domain–likedsDNA
74748a.154.1ABVVariable surface antigen VlsEdsDNA
143602d.321.1ABEVSTIV B116-likedsDNA
58064h.3.1ABEVInfluenza hemagglutinin (stalk)dsDNA, minus-ssRNA