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RdRp

Euk-Vir

Hubei_permutotetra-like_virus_1

RdRp__YP_009337300__Hubei_permutotetra-like_virus_1__1923073

Identity

Accession:
YP_009337300 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

74.0 mean pLDDT

Cluster

View cluster (20 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 318-365_451-526
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D328-384_485-539
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 76.7 2.20e-21 54.8% 17.9%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8adbA01 3.90.70.120 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.67 42.0 3.48e-01 91.1% 36.7%
2kgyA00 3.30.505.20 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › 0.62 35.0 3.94e-01 90.3% 72.8%
2it9A00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.60 38.0 3.93e-01 96.8% 65.0%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.60 37.0 3.76e-01 94.4% 62.5%
5upiA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.59 34.0 2.92e-01 74.2% 36.7%
1vgyA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.56 46.0 3.70e-01 90.3% 99.2%
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.54 27.0 3.68e-01 70.2% 93.7%
1o7dD01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.51 38.0 3.02e-01 77.4% 49.8%
4bwgD00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 29.0 3.24e-01 78.2% 71.1%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3616330 77.3.1.4 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › PF28998 0.62 27.0 2.66e-01 74.2% 37.0%
3929256 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.60 40.0 3.92e-01 95.2% 60.7%
3103201 2003.1.9.4 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF+UBA_E1_SCCH 0.54 38.0 2.56e-01 72.6% 71.8%
3739822 12.3.1.9 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Glyco_hydro_81 0.52 39.0 2.92e-01 79.0% 44.8%
3618481 247.1.1.5 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B,HAGH_C 0.51 40.0 2.93e-01 83.1% 65.6%
3397105 12.3.1.13 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Glyco_hydro_38C 0.51 38.0 2.89e-01 79.0% 50.7%
D2 high residues 803-924
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l6mA00 3.30.160.400 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 46.0 4.98e-01 72.1% 86.1%
4n4rB00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.57 40.0 3.81e-01 73.0% 96.0%
3bghB01 3.30.160.180 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Putative neuraminyllactose-binding hemagglutinin homolog like domain 0.57 42.0 3.75e-01 76.2% 97.7%
6d92A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 40.0 3.17e-01 73.8% 45.9%
4i4kA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 33.0 3.21e-01 93.4% 55.8%
3f7sA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 33.0 3.17e-01 97.5% 55.6%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3701914 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.71 49.0 5.45e-01 88.5% 90.5%
3258452 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.71 49.0 4.95e-01 86.1% 71.7%
4444614 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.69 45.0 5.32e-01 74.6% 100.0%
3456246 330.1.1.19 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DSRM_2 0.65 45.0 5.08e-01 86.1% 95.6%
3305941 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 48.0 4.93e-01 86.1% 81.7%
5004264 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.63 44.0 4.42e-01 71.3% 81.3%
3797649 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 48.0 5.09e-01 91.0% 90.0%
4278326 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.62 44.0 4.25e-01 72.1% 91.9%
3345144 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.62 36.0 4.45e-01 73.0% 93.3%
4472716 330.1.1.3 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.62 48.0 4.69e-01 86.9% 76.2%
3609908 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 49.0 5.13e-01 86.1% 98.2%
4393122 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.60 43.0 4.29e-01 73.0% 78.4%
3595183 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 33.0 4.03e-01 75.4% 86.7%
3718419 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.59 53.0 4.61e-01 98.4% 75.5%
4087100 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.59 36.0 4.21e-01 75.4% 91.3%
4954798 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.58 42.0 4.22e-01 73.8% 80.5%
4237498 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.57 40.0 4.06e-01 73.0% 70.4%
4507935 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.57 39.0 3.93e-01 71.3% 69.1%
4878112 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.57 34.0 3.67e-01 73.0% 69.9%
4958682 504.1.1.0 ↗ a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB 0.56 41.0 4.02e-01 75.4% 82.3%
3336892 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.56 40.0 4.02e-01 74.6% 78.4%
4579550 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.54 39.0 3.88e-01 75.4% 71.5%
1954221 2.26.1.1 ↗ beta barrels › OB-fold › Arcadin-1 › Arcadin-1 › Arcadin_1 0.53 31.0 3.80e-01 91.8% 93.3%
4289288 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.52 41.0 4.08e-01 84.4% 78.1%
3305808 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.52 44.0 2.84e-01 91.8% 37.3%
3832543 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.52 43.0 2.64e-01 91.8% 32.1%
3834362 3832.1.1.2 ↗ alpha bundles › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › PF25968 0.52 43.0 2.86e-01 91.8% 52.0%
2123814 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.52 33.0 3.66e-01 71.3% 78.8%
4939419 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.52 33.0 3.89e-01 71.3% 92.9%
3912315 5.1.4.371 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Frtz 0.52 40.0 2.70e-01 81.1% 40.2%
3972242 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.51 40.0 3.67e-01 83.6% 92.7%
5013602 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.50 32.0 3.64e-01 70.5% 87.8%
D3 medium residues 43-70_119-137_537-547_561-609
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22260.2 best Permu_RdRp_thumb 65.6 5.30e-18 54.2% 47.6%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u61D03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.53 27.0 2.94e-01 74.8% 54.9%
3l4aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.53 37.0 3.61e-01 72.9% 91.7%
1f68A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 38.0 3.92e-01 76.6% 100.0%
1wfdA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.50 35.0 3.78e-01 78.5% 82.8%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4003246 5067.1.1.5 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Sterol-sensing 0.54 39.0 3.34e-01 75.7% 74.4%
4192182 102.1.1.10 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › DNA_ligase_ZBD,HHH_2 0.51 41.0 3.48e-01 89.7% 88.4%
3221588 188.1.1.0 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain 0.51 45.0 3.47e-01 97.2% 80.8%
D4 medium residues 71-118_138-168_205-292_417-442_548-560
PDB
Domain cluster: rep: NIb__YP_009221991__Jasmine_virus_T__1775963__D1-51_64-80_112-210_276-312
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 139.2 2.20e-40 44.2% 24.9%
PF22152.2 Permu_RdRp_palm 33.4 3.10e-08 18.9% 8.1%
D5 medium residues 169-204_293-304_366-416
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 70.9 1.20e-19 57.6% 14.8%
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1x9fD00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 45.0 3.98e-01 74.7% 94.3%
2nrlA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 46.0 4.00e-01 77.8% 95.2%
3mxtA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.57 35.0 3.53e-01 100.0% 61.0%
2yorA00 1.10.489.10 Mainly Alpha › Orthogonal Bundle › Chloroperoxidase › Chloroperoxidase-like 0.56 41.0 2.92e-01 78.8% 72.5%
2h8oA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 39.0 2.80e-01 72.7% 78.1%
3uonA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.54 40.0 2.95e-01 79.8% 71.7%
2vj4A01 1.10.10.2060 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.52 40.0 4.19e-01 97.0% 92.2%
2p11A02 1.10.286.50 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.52 30.0 3.35e-01 74.7% 74.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3898876 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.60 44.0 3.90e-01 77.8% 95.2%
3279580 106.1.1.6 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › MPAB_Lcp_cat 0.58 41.0 3.03e-01 74.7% 54.3%
161069 141.1.1.1 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › polyprenyl_synt 0.55 39.0 2.80e-01 72.7% 78.1%
3671176 4230.1.1.6 ↗ alpha arrays › DnaD domain › DnaD domain › DnaD domain › Init_tRNA_PT 0.54 41.0 4.09e-01 97.0% 80.0%
4990011 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.53 42.0 3.08e-01 89.9% 74.5%
5021698 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.52 40.0 3.00e-01 83.8% 84.2%
3691125 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.51 44.0 3.98e-01 96.0% 80.0%
5053783 5082.1.1.0 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like 0.50 37.0 3.28e-01 78.8% 70.7%