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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_narna-like_virus_18

RNA-dependent_RNA_polymerase__YP_009330065__Hubei_narna-like_virus_18__1922948

Identity

Accession:
YP_009330065 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

80.7 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 1-93
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.63 44.0 4.83e-01 82.8% 89.5%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.63 39.0 4.35e-01 81.7% 79.7%
8b6jF01 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.56 32.0 3.72e-01 79.6% 79.1%
4iu9B02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.55 48.0 3.81e-01 100.0% 82.3%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.54 42.0 3.61e-01 82.8% 63.4%
4hxiB03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.53 40.0 3.95e-01 82.8% 74.7%
2v0cA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.52 40.0 3.39e-01 82.8% 74.2%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.52 41.0 3.57e-01 100.0% 54.8%
2nsfA01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.51 46.0 3.79e-01 97.8% 89.9%
7e84A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 38.0 3.52e-01 81.7% 82.1%
4ib4A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.50 44.0 3.17e-01 100.0% 58.9%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3304034 5050.1.1.42 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › GDT1 0.64 58.0 4.40e-01 100.0% 93.5%
4988250 3745.1.1.1 alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.62 52.0 3.63e-01 94.6% 68.4%
4011047 5050.1.1.1 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.59 53.0 3.95e-01 100.0% 71.5%
3537204 5050.1.1.22 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1_like 0.54 47.0 3.69e-01 100.0% 84.7%
4928642 1075.1.2.0 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.53 39.0 3.46e-01 94.6% 52.1%
3688973 2004.1.1.250 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.53 46.0 2.97e-01 97.8% 95.2%
3483292 5050.1.1.0 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 47.0 3.72e-01 100.0% 81.0%
3540796 5050.1.1.32 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Acatn 0.52 45.0 3.65e-01 100.0% 84.6%
56815 620.1.1.0 alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases 0.51 46.0 3.80e-01 97.8% 88.1%
4033 620.1.1.5 alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › MDMPI_N 0.51 46.0 3.79e-01 97.8% 89.4%
3288662 620.1.1.5 alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › MDMPI_N 0.50 45.0 3.76e-01 96.8% 86.5%
D2 medium residues 96-147_214-259_290-363
PDB
Domain cluster: representative
CATH (4)
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 0.79 72.0 5.04e-01 96.5% 62.5%
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.75 64.0 6.36e-01 89.0% 100.0%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.51 29.0 3.75e-01 95.3% 99.0%
2ou3A01 1.10.3680.10 Mainly Alpha › Orthogonal Bundle › TerB-like › TerB-like 0.51 30.0 3.19e-01 77.9% 64.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5367 304.48.1.8 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.85 80.0 6.05e-01 100.0% 74.1%
5364 304.48.1.8 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.84 80.0 5.99e-01 100.0% 70.5%
5366 304.48.1.15 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 0.83 78.0 5.81e-01 100.0% 66.8%
4152428 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.82 57.0 4.40e-01 70.9% 61.1%
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 0.79 72.0 5.39e-01 96.5% 80.3%
217141 304.48.1.15 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 0.79 75.0 5.75e-01 100.0% 72.0%
1697857 304.48.1.30 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › CPV_RdRP_pol_dom 0.77 70.0 5.50e-01 96.5% 96.2%
3097450 304.48.1.12 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol 0.77 67.0 4.99e-01 90.7% 81.8%
3960648 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.77 55.0 4.49e-01 73.3% 69.5%
3693017 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.77 71.0 5.39e-01 97.7% 84.6%
3209439 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.77 69.0 5.55e-01 95.9% 82.2%
3589612 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.77 58.0 4.56e-01 77.3% 67.9%
3260077 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.76 72.0 5.38e-01 100.0% 75.1%
4497954 304.48.1.73 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1, RVT_N 0.75 57.0 4.60e-01 77.9% 85.8%
4019374 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.75 70.0 5.23e-01 99.4% 78.5%
4461237 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.75 57.0 3.94e-01 77.9% 41.4%
5018583 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.74 57.0 4.52e-01 77.9% 84.4%
5002351 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.72 55.0 4.16e-01 78.5% 58.7%
3615476 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.68 62.0 4.90e-01 95.3% 79.4%
4070164 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.64 54.0 4.18e-01 88.4% 73.1%
4138932 304.48.1.72 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_N 0.63 47.0 3.88e-01 76.7% 72.3%
3929906 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.62 46.0 4.05e-01 98.8% 53.1%
4976198 878.1.1.1 a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.54 22.0 3.11e-01 90.1% 75.3%
D3 medium residues 148-213
PDB
D4 medium residues 260-289_364-458
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05919.17 best Mitovir_RNA_pol 25.5 9.40e-06 77.6% 10.9%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 54.0 5.87e-01 100.0% 99.1%
4hkqA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.64 58.0 5.49e-01 99.2% 82.6%
2qyxB01 3.30.70.1360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › mj0159-like 0.53 34.0 3.63e-01 81.6% 73.4%
1vk8A00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 4.28e-01 81.6% 98.9%
1lxnA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 4.23e-01 80.0% 98.0%
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 38.0 4.20e-01 81.6% 96.1%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4064506 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.69 34.0 4.76e-01 73.6% 98.3%
4265513 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.68 33.0 4.66e-01 73.6% 98.3%
4073486 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.65 36.0 4.23e-01 77.6% 75.6%
4358505 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.63 35.0 4.15e-01 77.6% 78.8%
4267491 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.63 36.0 4.09e-01 78.4% 73.7%
1827765 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.62 57.0 4.27e-01 100.0% 62.2%
4449545 304.48.1.39 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › MatK_N 0.62 55.0 3.97e-01 97.6% 67.9%
4949196 304.117.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC 0.60 30.0 4.21e-01 76.8% 100.0%
3947863 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.60 52.0 4.08e-01 93.6% 70.6%
3934202 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.59 51.0 4.89e-01 92.8% 100.0%
3926633 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 51.0 4.47e-01 96.8% 75.7%
4173742 304.117.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC 0.55 33.0 4.17e-01 79.2% 100.0%
5023633 304.24.1.5 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.55 31.0 3.97e-01 80.8% 98.6%
4309637 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 0.53 33.0 3.84e-01 74.4% 90.5%
4981261 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.53 32.0 3.97e-01 77.6% 100.0%
5069565 304.26.1.0 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like 0.53 39.0 4.39e-01 80.8% 100.0%
3254951 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 33.0 3.63e-01 83.2% 81.6%
5007807 304.26.1.1 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.51 36.0 4.13e-01 80.8% 97.9%
D5 medium residues 459-566_644-670
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5z62E00 1.25.40.40 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI 0.63 32.0 3.55e-01 88.1% 59.6%
1eguA02 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.51 45.0 3.34e-01 100.0% 65.3%
2wcoA01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.51 45.0 3.35e-01 100.0% 62.3%
3p1uA00 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.50 43.0 3.00e-01 97.0% 57.5%
6ljaA01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.50 44.0 3.32e-01 100.0% 53.6%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3227167 109.4.1.451 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Iml2-TPR_39 0.52 46.0 3.65e-01 98.5% 73.6%
3821367 109.4.1.1304 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_10, TPR_12 0.50 42.0 3.75e-01 94.1% 68.3%
D6 medium residues 567-643
PDB