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RNA-dependent_RNA_polymerase

Euk-Vir

Wenling_narna-like_virus_2

RNA-dependent_RNA_polymerase__YP_009337193__Wenling_narna-like_virus_2__1923502

Identity

Accession:
YP_009337193 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

73.6 mean pLDDT

Cluster

View cluster (39 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 66-190
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337264__Wenling_narna-like_virus_1__1923501__D1-107
D2 medium residues 235-379
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009333139__Beihai_narna-like_virus_22__1922450__D259-367
D3 medium residues 380-417_476-581
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.76 59.0 6.37e-01 79.9% 95.9%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.73 56.0 5.91e-01 80.6% 96.9%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 54.0 5.93e-01 77.1% 97.4%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 51.0 5.89e-01 77.1% 100.0%
1pfsA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.71 21.0 2.84e-01 84.7% 47.4%
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.71 37.0 5.01e-01 85.4% 97.3%
1mw7A03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.71 38.0 5.05e-01 72.9% 100.0%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.69 37.0 4.88e-01 84.7% 100.0%
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 47.0 5.36e-01 96.5% 95.3%
3trgA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 40.0 4.78e-01 85.4% 91.5%
4j37A01 3.30.70.580 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, N-terminal subdomain 0.62 44.0 5.01e-01 86.1% 98.2%
1yqhA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 41.0 4.66e-01 86.8% 92.3%
1mg7A01 3.30.70.1000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Switch protein XOL-1, GHMP-like 0.59 42.0 3.97e-01 74.3% 85.1%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.58 38.0 4.53e-01 82.6% 100.0%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 38.0 4.45e-01 81.2% 94.9%
1p50A02 3.30.590.10 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › Glutamine synthetase/guanido kinase, catalytic domain 0.54 44.0 3.68e-01 88.9% 80.4%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.54 43.0 3.61e-01 83.3% 94.1%
3i4hX01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 43.0 4.59e-01 86.1% 100.0%
3gqcC01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.53 42.0 4.36e-01 84.0% 94.9%
4hacA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.50 36.0 3.78e-01 72.9% 88.4%
1cg2A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 36.0 4.02e-01 73.6% 99.1%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4293970 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.81 43.0 5.88e-01 71.5% 100.0%
4093818 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.73 37.0 4.99e-01 86.8% 94.7%
3810170 304.48.1.43 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol 0.71 67.0 6.13e-01 99.3% 96.1%
4070496 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.70 37.0 5.03e-01 86.8% 100.0%
4080258 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.68 37.0 4.85e-01 86.1% 100.0%
4942434 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.64 42.0 5.04e-01 77.1% 100.0%
4519288 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.64 36.0 4.66e-01 84.7% 100.0%
3227297 11.10.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like 0.63 25.0 2.71e-01 100.0% 41.5%
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 0.63 56.0 4.57e-01 95.8% 68.2%
3408148 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.62 43.0 4.40e-01 70.8% 78.6%
4552975 304.102.1.3 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_1 0.62 43.0 3.78e-01 71.5% 100.0%
4254800 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.61 42.0 4.84e-01 81.9% 100.0%
4021804 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.60 36.0 4.37e-01 70.1% 90.5%
3961696 304.48.1.48 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF_2 0.59 46.0 4.59e-01 81.9% 84.0%
3585792 304.51.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.57 39.0 4.43e-01 94.4% 91.8%
3813645 304.9.1.9 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_2 0.54 40.0 3.58e-01 86.1% 53.8%
4355727 304.9.1.71 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › SNU71_RBD 0.53 39.0 4.04e-01 84.0% 79.3%
4221300 304.9.1.109 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PF28459 0.53 37.0 3.81e-01 86.8% 74.8%
4586646 230.1.1.5 ↗ a+b two layers › T-fold › Tetrahydrobiopterin biosynthesis enzymes-like › Tetrahydrobiopterin biosynthesis enzymes-like › GCHY-1 0.53 36.0 3.85e-01 97.2% 79.2%
4629438 230.1.1.5 ↗ a+b two layers › T-fold › Tetrahydrobiopterin biosynthesis enzymes-like › Tetrahydrobiopterin biosynthesis enzymes-like › GCHY-1 0.51 35.0 3.89e-01 95.8% 90.9%
3678022 2004.1.1.29 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 0.51 35.0 3.23e-01 70.8% 84.7%
5033367 304.20.1.4 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.50 44.0 4.08e-01 95.8% 95.7%
4120121 230.1.1.5 ↗ a+b two layers › T-fold › Tetrahydrobiopterin biosynthesis enzymes-like › Tetrahydrobiopterin biosynthesis enzymes-like › GCHY-1 0.50 34.0 3.85e-01 95.8% 90.9%
D4 medium residues 418-475
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6h9dA00 1.10.530.40 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.65 40.0 3.02e-01 100.0% 24.3%
2ab5B01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.62 39.0 3.04e-01 96.6% 28.9%
1dgmA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.61 40.0 2.56e-01 100.0% 14.1%
3es1A01 2.20.70.150 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.55 34.0 3.76e-01 94.8% 94.6%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.54 43.0 2.65e-01 91.4% 79.9%
3mr0A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 34.0 2.74e-01 96.6% 34.5%
6ketA01 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.53 38.0 2.36e-01 75.9% 41.7%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.52 42.0 3.24e-01 100.0% 63.0%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.51 43.0 2.88e-01 100.0% 44.5%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 36.0 2.60e-01 79.3% 80.8%
5f3bD00 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.50 36.0 2.97e-01 75.9% 91.3%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4003509 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 0.76 65.0 4.75e-01 100.0% 36.1%
3810170 304.48.1.43 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol 0.75 65.0 4.59e-01 100.0% 31.7%
3251965 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 0.67 54.0 3.64e-01 100.0% 22.5%
3651060 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 0.67 57.0 4.06e-01 100.0% 32.6%
3258201 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 0.66 55.0 3.78e-01 100.0% 26.4%
4289835 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 0.65 54.0 3.82e-01 100.0% 29.0%
3674655 2003.1.9.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins 0.65 51.0 3.01e-01 100.0% 9.5%
3272304 304.36.1.2 ↗ a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1 0.65 51.0 4.00e-01 100.0% 37.2%
3622284 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.65 41.0 2.41e-01 82.8% 8.3%
3911603 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 0.63 52.0 3.90e-01 100.0% 37.6%
3194847 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.63 41.0 2.36e-01 82.8% 6.2%
3650065 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 51.0 3.44e-01 100.0% 23.8%
4061408 109.4.1.1731 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N 0.61 36.0 2.15e-01 82.8% 6.9%
3960213 304.156.1.5 ↗ a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain › PF31086 0.60 34.0 2.76e-01 96.6% 26.1%
3261509 109.4.1.890 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C 0.60 37.0 2.10e-01 82.8% 5.1%
3988925 3227.1.1.1 ↗ alpha complex topology › phosphorylation-coupled saccharide transporter ChbC › phosphorylation-coupled saccharide transporter ChbC › phosphorylation-coupled saccharide transporter ChbC › PTS_EIIC 0.60 50.0 3.05e-01 100.0% 32.9%
3190533 109.4.1.3564 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C, HAT_PRP39_N, HAT_PRP39_C 0.59 36.0 2.13e-01 82.8% 6.9%
3687833 5073.1.1.18 ↗ alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain M › Hydrolase 0.59 52.0 2.97e-01 100.0% 44.0%
5018509 2008.1.1.15 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.58 41.0 2.68e-01 74.1% 42.0%
4000704 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 0.58 45.0 3.39e-01 100.0% 30.0%
None — 0.57 41.0 2.26e-01 81.0% 38.5%
3586428 306.3.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like 0.55 39.0 3.35e-01 100.0% 43.1%
4198 4970.1.1.3 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B_2 0.54 37.0 3.61e-01 70.7% 92.3%
3890428 109.3.1.96 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank+Ank_2+Ank_4 0.54 39.0 2.83e-01 77.6% 40.0%
3584696 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 41.0 2.34e-01 81.0% 11.1%
57748 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.54 37.0 3.57e-01 70.7% 92.3%
4639306 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.53 40.0 2.31e-01 86.2% 8.3%
3950094 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.53 43.0 2.87e-01 100.0% 66.2%
4315154 3294.1.1.1 ↗ alpha complex topology › FAS type I helical domain › FAS type I helical domain › FAS type I helical domain › FAS_I_H 0.53 38.0 2.73e-01 79.3% 77.1%
4595166 5076.2.1.0 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ 0.53 38.0 2.68e-01 96.6% 20.9%
3509042 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 36.0 2.83e-01 72.4% 37.7%
3519143 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.52 36.0 2.39e-01 75.9% 25.9%
3311607 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.52 35.0 2.97e-01 100.0% 37.3%
4007581 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 35.0 3.68e-01 93.1% 82.0%
3974680 2006.1.3.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain 0.52 40.0 2.93e-01 89.7% 82.2%
4991918 632.18.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.51 44.0 3.67e-01 100.0% 64.8%
3594033 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 0.51 43.0 2.95e-01 100.0% 40.0%
3739386 109.4.1.3152 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, TPR_16, TPR_19, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_N 0.51 36.0 2.07e-01 77.6% 9.5%
3523834 5.1.4.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CNH 0.50 39.0 2.47e-01 89.7% 93.7%
D5 medium residues 582-654
PDB
D6 medium residues 655-741
PDB