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RdRp

Euk-Vir

Wuhan_Millipede_virus_4

RdRp__YP_009342308__Wuhan_Millipede_virus_4__1923689

Identity

Accession:
YP_009342308 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

84.8 mean pLDDT

Taxonomy

TaxID: 1923689

3D Structure

Domains

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

D1 medium residues 88-149
PDB
Domain cluster: representative
D2 medium residues 150-246_273-358
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 59.8 2.90e-16 53.5% 16.2%
D3 medium residues 247-272_427-550
PDB
D4 medium residues 359-426
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.81 74.0 6.32e-01 100.0% 68.9%
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.80 72.0 6.02e-01 100.0% 61.2%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.78 70.0 5.46e-01 100.0% 52.8%
1vbkA01 3.30.70.1510 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like 0.71 56.0 5.32e-01 100.0% 72.3%
2xmjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 52.0 5.43e-01 88.2% 85.7%
2zueA01 3.30.1360.70 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Arginyl tRNA synthetase N-terminal domain 0.70 58.0 4.98e-01 95.6% 72.2%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.67 51.0 5.12e-01 95.6% 82.6%
3kewB02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.67 57.0 4.59e-01 100.0% 85.4%
1h3dA03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 50.0 5.04e-01 97.1% 83.6%
1fvqA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 53.0 5.29e-01 95.6% 86.1%
5zneA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 54.0 5.34e-01 97.1% 87.7%
1whyA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.65 54.0 5.33e-01 94.1% 90.3%
1vi7A02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 51.0 5.05e-01 97.1% 85.9%
4noiA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.64 47.0 4.22e-01 82.4% 69.9%
1in0A01 3.30.70.860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 51.0 5.08e-01 98.5% 88.6%
3cjsA00 3.30.70.1170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sun protein; domain 3 0.63 42.0 4.48e-01 97.1% 82.8%
1wf1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.62 50.0 4.63e-01 95.6% 68.9%
3aqoA01 3.30.70.3400 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 53.0 5.06e-01 100.0% 82.5%
1weyA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.62 52.0 4.64e-01 100.0% 67.3%
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.61 47.0 4.65e-01 97.1% 80.0%
2g9oA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 4.85e-01 98.5% 83.1%
7uvpA02 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.60 47.0 4.75e-01 92.6% 85.5%
1wg4A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 50.0 4.92e-01 98.5% 88.3%
7l9pK01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.60 40.0 3.38e-01 82.4% 40.3%
2j0wA04 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 49.0 4.77e-01 95.6% 85.3%
3oreA01 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.59 42.0 4.32e-01 79.4% 80.3%
1ghhA00 3.30.910.10 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › DinI-like 0.58 45.0 4.25e-01 83.8% 75.3%
3na2A00 3.40.1570.20 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › 0.58 46.0 3.72e-01 89.7% 94.2%
2jsxA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.58 45.0 4.46e-01 95.6% 84.5%
2vd3A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 44.0 4.40e-01 95.6% 81.1%
2dy1A03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.56 44.0 4.29e-01 91.2% 77.6%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.55 46.0 4.20e-01 94.1% 75.5%
1usuB00 3.15.10.20 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Activator of Hsp90 ATPase Aha1, N-terminal domain 0.55 48.0 3.92e-01 100.0% 66.7%
3ltoA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.55 42.0 3.47e-01 92.6% 44.0%
2vycA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 40.0 2.95e-01 79.4% 76.8%
1lk5A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 42.0 4.09e-01 91.2% 84.8%
2y3mA02 3.30.1370.130 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.52 35.0 3.67e-01 75.0% 85.7%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 42.0 3.69e-01 98.5% 77.2%
7dklA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 44.0 4.08e-01 100.0% 84.4%
8a5eD01 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 39.0 3.78e-01 88.2% 78.5%
1darA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 42.0 2.89e-01 95.6% 28.7%
ECOD (65)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4946635 309.1.2.1 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.76 68.0 5.20e-01 100.0% 84.5%
3971560 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.71 59.0 5.99e-01 97.1% 96.9%
5072747 304.120.1.6 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.71 56.0 5.84e-01 100.0% 98.3%
5076763 304.120.1.6 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.69 55.0 5.34e-01 100.0% 78.7%
5054216 309.1.2.1 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.69 59.0 4.72e-01 100.0% 89.7%
5012054 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.68 56.0 5.56e-01 91.2% 92.9%
3766704 309.1.2.1 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.68 58.0 4.47e-01 100.0% 77.6%
4987730 1.1.5.44 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › SecDF_P1_head 0.68 58.0 4.20e-01 97.1% 93.5%
3810151 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.67 52.0 5.20e-01 95.6% 84.3%
4209732 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.66 57.0 5.20e-01 100.0% 82.1%
3968877 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.66 54.0 5.29e-01 97.1% 85.3%
3428671 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.66 54.0 5.44e-01 94.1% 92.9%
5080599 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 48.0 4.95e-01 94.1% 86.2%
3667032 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 52.0 5.15e-01 95.6% 84.0%
4006107 304.8.1.2 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.65 54.0 5.26e-01 97.1% 85.3%
4948608 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 49.0 4.99e-01 97.1% 87.7%
3957783 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.65 50.0 4.97e-01 92.6% 84.3%
4985138 304.120.1.6 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.65 50.0 4.68e-01 94.1% 68.2%
3964348 304.28.1.3 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD-TM1 0.65 52.0 5.12e-01 98.5% 82.7%
4997766 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 52.0 4.60e-01 92.6% 80.0%
3710411 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.64 51.0 5.36e-01 94.1% 100.0%
5062182 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.64 50.0 5.09e-01 97.1% 90.8%
5023739 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 56.0 4.88e-01 100.0% 78.1%
5029986 3261.1.1.0 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb 0.64 47.0 5.07e-01 85.3% 100.0%
3588365 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.64 44.0 4.12e-01 80.9% 57.6%
3658421 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.63 50.0 4.87e-01 97.1% 80.0%
3967558 306.6.1.1 a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like › CT_C_D 0.63 48.0 4.50e-01 83.8% 69.4%
4970952 3715.1.1.1 a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal_L22e 0.63 53.0 5.02e-01 98.5% 82.4%
4419939 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.63 53.0 5.05e-01 97.1% 81.2%
4191065 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.63 50.0 4.93e-01 98.5% 84.0%
4936518 304.128.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.62 46.0 4.48e-01 94.1% 74.7%
4957408 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.62 50.0 4.44e-01 94.1% 81.9%
3392977 304.55.2.9 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › DUF4780 0.62 52.0 4.86e-01 100.0% 82.2%
4636695 304.36.1.1 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.61 49.0 4.95e-01 95.6% 91.2%
3163733 304.24.1.2 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › DUF1949 0.61 46.0 4.66e-01 89.7% 82.9%
5077572 304.128.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.61 47.0 4.59e-01 92.6% 77.3%
4963940 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.61 45.0 4.56e-01 85.3% 80.0%
3621974 327.11.2.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.61 43.0 4.23e-01 79.4% 69.3%
3164240 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.60 50.0 4.97e-01 97.1% 92.9%
4935680 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.60 49.0 4.32e-01 95.6% 79.1%
4978356 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.60 48.0 4.81e-01 98.5% 88.6%
5027911 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.60 51.0 4.58e-01 100.0% 81.0%
4937870 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.60 49.0 4.50e-01 97.1% 83.2%
5044372 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.59 48.0 4.25e-01 95.6% 76.4%
4159102 304.14.1.0 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.59 48.0 4.81e-01 97.1% 90.0%
5007661 7584.1.1.1 a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding 0.59 43.0 2.98e-01 77.9% 60.0%
5082182 304.128.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.59 46.0 4.22e-01 91.2% 63.2%
4928456 306.6.1.0 a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.59 40.0 4.12e-01 72.1% 87.7%
4528041 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.59 42.0 4.44e-01 82.4% 88.3%
5077636 304.128.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.59 45.0 4.35e-01 98.5% 73.8%
5036986 327.11.1.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.58 45.0 4.70e-01 94.1% 100.0%
5078527 304.128.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.58 47.0 4.49e-01 98.5% 76.5%
5050596 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.58 46.0 4.60e-01 98.5% 90.0%
4930178 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.57 48.0 4.21e-01 100.0% 75.5%
4932655 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.57 44.0 4.54e-01 91.2% 95.4%
4946403 3646.1.1.1 alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.56 44.0 3.03e-01 83.8% 84.2%
5078551 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 40.0 4.24e-01 80.9% 86.7%
4929334 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.56 43.0 4.36e-01 97.1% 87.1%
5072608 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.55 45.0 4.41e-01 97.1% 85.3%
5016606 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 42.0 3.47e-01 91.2% 43.6%
5031760 304.4.1.19 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › SCO4226-like 0.54 45.0 4.27e-01 98.5% 84.7%
4306133 3016.1.1.10 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › GDC-P 0.54 44.0 4.04e-01 98.5% 68.8%
3280548 306.6.1.0 a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.53 38.0 3.71e-01 80.9% 68.8%
4654615 325.1.7.2 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RNA_pol_Rpb2_6 0.53 40.0 2.79e-01 82.4% 33.0%
3590102 2005.1.1.11 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.51 37.0 2.57e-01 76.5% 91.3%