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VP2

Euk-Vir

Fall_chinook_aquareovirus

VP2__YP_009351850__Fall_chinook_aquareovirus__1963254

Identity

Accession:
YP_009351850 ↗
Protein ID:
VP2
Kingdom:
euk

Quality

89.3 mean pLDDT

Cluster

View cluster (29 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 281-381
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 139.8 1.00e-40 100.0% 8.0%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4jylA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.60 27.0 3.60e-01 100.0% 83.7%
6h5hA00 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.56 33.0 3.88e-01 84.2% 83.1%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.56 43.0 3.85e-01 82.2% 94.5%
3r8eA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 30.0 2.71e-01 100.0% 40.7%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2392232 4963.1.1.2 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_5 0.98 96.0 6.11e-01 100.0% 26.2%
4905 4963.1.1.2 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_5 0.94 90.0 5.79e-01 100.0% 26.4%
3600382 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 41.0 2.47e-01 87.1% 22.3%
D2 medium residues 33-164
PDB
Domain cluster: rep: core_RNA-dependent_RNA_polymerase__YP_009445963__Piscine_orthoreovirus__1157337__D63-154_212-236
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 137.5 4.90e-40 100.0% 10.3%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2392232 4963.1.1.2 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_5 0.96 94.0 6.37e-01 100.0% 34.3%
4905 4963.1.1.2 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_5 0.94 92.0 6.27e-01 100.0% 35.1%
D3 medium residues 182-269
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 100.9 5.40e-29 100.0% 6.8%
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1sxjB03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.75 51.0 5.04e-01 97.7% 66.3%
1j3wC00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.66 46.0 4.01e-01 72.7% 98.5%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 47.0 4.88e-01 100.0% 85.5%
3oduB01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.62 56.0 3.92e-01 100.0% 34.7%
1gjsA00 1.10.8.40 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Albumin-binding domain 0.60 34.0 3.85e-01 100.0% 73.8%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 44.0 4.12e-01 79.5% 63.3%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 44.0 4.32e-01 78.4% 75.5%
1mw9X02 1.10.460.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 0.58 50.0 4.18e-01 98.9% 93.9%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.58 38.0 3.76e-01 97.7% 62.1%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.57 50.0 4.47e-01 95.5% 75.4%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 42.0 3.99e-01 79.5% 65.1%
2hezA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.56 49.0 3.39e-01 100.0% 79.0%
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.55 38.0 3.83e-01 71.6% 75.8%
2bjfA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.54 48.0 3.27e-01 98.9% 79.9%
2itmB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 41.0 3.04e-01 81.8% 31.2%
1yf2A02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.54 36.0 3.41e-01 79.5% 56.1%
3g2bA00 1.10.10.1150 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD) 0.53 34.0 3.45e-01 72.7% 63.3%
3clmA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.53 42.0 2.90e-01 89.8% 76.4%
1yowA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.53 45.0 3.34e-01 94.3% 57.0%
5owcA00 1.20.90.10 Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain 0.53 46.0 4.14e-01 96.6% 82.0%
4ovjA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 46.0 3.47e-01 98.9% 78.1%
3r7wB02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 35.0 3.28e-01 73.9% 100.0%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2392232 4963.1.1.2 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_5 0.98 94.0 5.87e-01 100.0% 22.6%
4992926 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.70 49.0 5.26e-01 100.0% 85.3%
5046776 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.69 49.0 5.57e-01 100.0% 98.5%
5027497 632.6.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit 0.67 51.0 5.38e-01 100.0% 90.0%
3603132 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.67 47.0 4.87e-01 100.0% 80.0%
5078448 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.61 45.0 4.20e-01 79.5% 62.7%
3996626 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.60 44.0 4.47e-01 98.9% 78.7%
4940192 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.59 44.0 4.01e-01 78.4% 70.2%
3937187 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.59 44.0 4.04e-01 79.5% 62.7%
3592519 2004.5.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain 0.58 52.0 3.98e-01 97.7% 88.4%
3475061 103.1.1.3 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › CRAL_TRIO_N 0.56 35.0 3.92e-01 100.0% 86.2%
3932018 168.1.1.0 ↗ alpha arrays › Sec7 domain › Sec7 domain › Sec7 domain 0.55 42.0 2.41e-01 98.9% 7.8%
3279916 633.21.1.34 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › DUF7144 0.55 47.0 4.37e-01 97.7% 73.9%
3322847 5050.1.1.2 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › PTR2 0.54 47.0 2.91e-01 100.0% 86.2%
3699939 2006.1.6.13 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA_3 0.53 46.0 3.62e-01 100.0% 89.7%
3445477 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.52 45.0 3.66e-01 94.3% 83.1%
D4 medium residues 541-573_596-662
PDB
Domain cluster: rep: RNA_polymerase__YP_009110697__Cangyuan_orthoreovirus__1388882__D397-453_589-643
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 82.6 1.80e-23 69.0% 5.3%
PF07925.16 RdRP_5 44.5 5.90e-12 34.0% 2.6%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.93 90.0 5.46e-01 100.0% 23.9%
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.68 46.0 3.86e-01 100.0% 40.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5368 304.48.1.23 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_5 0.93 90.0 5.73e-01 100.0% 30.8%
3699975 6110.1.1.1 ↗ alpha superhelices › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › DHC_N2 0.55 37.0 2.31e-01 97.0% 12.7%
3718707 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 40.0 2.55e-01 84.0% 51.2%
4453818 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.51 38.0 3.35e-01 89.0% 52.7%
4809699 3781.1.1.1 ↗ a+b two layers › Ribosomal protein L11/L12e N-terminal domain-like › Ribosomal protein L11/L12e N-terminal domain › Ribosomal protein L11/L12e N-terminal domain › Ribosomal_L11_N 0.50 23.0 2.77e-01 100.0% 63.1%
D5 medium residues 574-595_693-787
PDB
Domain cluster: rep: RNA_polymerase__YP_009110697__Cangyuan_orthoreovirus__1388882__D557-588_685-792
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 125.0 3.00e-36 82.9% 7.5%
PF07925.16 RdRP_5 24.2 7.90e-06 19.7% 1.7%
D6 medium residues 903-949_1060-1092_1191-1274
PDB
Domain cluster: rep: VP2__YP_001837095__American_grass_carp_reovirus__465447__D1058-1114_1176-1274
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 69.7 1.40e-19 51.8% 6.6%
PF07925.16 RdRP_5 23.4 1.40e-05 29.9% 3.7%
PF07925.16 RdRP_5 30.6 9.50e-08 23.8% 2.8%
D7 medium residues 989-1015_1093-1190
PDB
Domain cluster: rep: VP2__YP_001837095__American_grass_carp_reovirus__465447__D966-1046_1125-1153
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07925.16 best RdRP_5 138.0 3.50e-40 82.4% 7.7%