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RNA-dependent_RNA_polymerase

Euk-Vir

Wenzhou_narna-like_virus_5

RNA-dependent_RNA_polymerase__YP_009337307__Wenzhou_narna-like_virus_5__1923580

Identity

Accession:
YP_009337307 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

73.8 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 62-185
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2d05A02 1.20.141.10 Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1 0.60 39.0 4.16e-01 100.0% 74.8%
4akgA06 1.10.8.710 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Dynein motor, AAA1 domain, small subdomain 0.57 42.0 4.44e-01 99.2% 87.9%
4ag6A02 1.10.8.730 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.55 41.0 4.36e-01 87.9% 89.1%
2pmiB00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 38.0 3.16e-01 73.4% 52.1%
6j95A01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 39.0 2.73e-01 79.8% 63.9%
7e4gA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.50 42.0 3.64e-01 92.7% 81.2%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4958530 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.65 49.0 5.22e-01 99.2% 93.3%
4939888 148.1.3.4 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › CbbQ_C 0.63 47.0 5.17e-01 96.8% 96.0%
2845180 2002.1.1.4 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Alpha-amylase 0.59 53.0 3.45e-01 99.2% 66.1%
3451722 3930.1.1.0 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.51 39.0 3.92e-01 89.5% 81.6%
D2 medium residues 186-248_320-373_395-459
PDB
Domain cluster: representative
CATH (1)
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 68.0 4.85e-01 91.2% 60.2%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3753267 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 68.0 5.03e-01 94.5% 63.9%
3258406 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 0.75 68.0 4.72e-01 96.2% 49.6%
3877925 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 0.75 66.0 5.09e-01 93.4% 70.6%
3789227 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 59.0 4.85e-01 83.0% 78.7%
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 0.72 63.0 4.92e-01 92.3% 81.6%
3615272 304.48.1.25 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.71 55.0 4.23e-01 79.1% 60.0%
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 0.71 61.0 5.01e-01 90.7% 78.8%
3598902 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 0.71 54.0 4.16e-01 78.0% 60.3%
3691350 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 0.70 61.0 5.28e-01 92.3% 92.2%
4516798 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 50.0 3.66e-01 74.2% 44.8%
3923013 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 0.68 54.0 4.30e-01 82.4% 64.6%
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 0.67 47.0 3.94e-01 70.9% 65.9%
3792091 304.48.1.25 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.67 51.0 4.08e-01 78.0% 59.7%
4424453 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 59.0 4.11e-01 94.0% 48.9%
4361688 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 58.0 4.49e-01 94.5% 69.3%
5018045 325.1.4.3 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Nicotinate/Quinolinate PRTase N-terminal domain-like › NAPRTase_N 0.50 25.0 2.76e-01 95.1% 55.5%
D3 medium residues 249-319
PDB
D4 medium residues 374-394_460-561
PDB
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.69 41.0 5.05e-01 90.2% 96.0%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.67 52.0 5.60e-01 84.6% 95.3%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.67 40.0 4.97e-01 90.2% 100.0%
1mw7A03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.65 40.0 4.92e-01 87.0% 100.0%
8b6jb01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.64 46.0 3.91e-01 75.6% 81.5%
2xhcA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.63 43.0 4.76e-01 88.6% 88.4%
4nnzA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.63 46.0 3.95e-01 75.6% 88.9%
1m1hA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.63 45.0 4.95e-01 91.9% 91.0%
1hi8A03 3.30.70.1600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 58.0 5.10e-01 100.0% 82.4%
4bbyA05 3.30.300.330 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.62 48.0 5.08e-01 80.5% 100.0%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 44.0 4.32e-01 78.0% 94.8%
2gffA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 41.0 4.56e-01 74.0% 93.8%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 42.0 4.69e-01 87.8% 100.0%
4dpoB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 40.0 4.41e-01 74.8% 90.1%
4l3tA03 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.57 45.0 3.73e-01 86.2% 77.0%
3gfaA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.56 44.0 3.74e-01 82.9% 76.0%
6pz0A01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.55 44.0 3.96e-01 82.9% 82.1%
5o60I00 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.55 44.0 4.42e-01 86.2% 86.5%
3viuA04 3.90.650.10 Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain 0.55 47.0 4.21e-01 94.3% 91.9%
1x7vA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 40.0 4.41e-01 86.2% 98.0%
3e8oB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 40.0 4.38e-01 86.2% 98.0%
3qjlA01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 4.51e-01 91.9% 100.0%
3k85A00 3.30.230.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 40.0 3.10e-01 86.2% 96.7%
2ymvA02 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.51 40.0 3.28e-01 82.9% 72.8%
1dt9A01 3.30.960.10 Alpha Beta › 2-Layer Sandwich › Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A › eRF1 domain 1 0.50 36.0 3.89e-01 74.8% 95.2%
5kfnA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.50 36.0 3.18e-01 73.2% 74.0%
4ammA00 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.50 42.0 2.98e-01 91.1% 60.7%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1279063 304.48.1.13 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.72 57.0 3.80e-01 82.9% 43.0%
4048587 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.71 41.0 5.24e-01 76.4% 100.0%
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 42.0 5.20e-01 89.4% 97.3%
4279811 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 40.0 4.86e-01 85.4% 87.5%
4875416 304.48.1.13 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.69 65.0 4.45e-01 100.0% 52.8%
4231349 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.69 40.0 5.11e-01 86.2% 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 0.69 41.0 5.03e-01 88.6% 96.0%
4678773 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 40.0 5.02e-01 89.4% 97.3%
4156338 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.67 40.0 4.94e-01 90.2% 97.3%
4357399 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.66 39.0 4.86e-01 80.5% 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 0.65 50.0 5.41e-01 83.7% 99.0%
4590927 304.28.1.2 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.64 45.0 5.20e-01 80.5% 100.0%
3924882 304.7.1.1 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 0.61 47.0 4.98e-01 87.0% 96.2%
3315278 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 49.0 4.91e-01 87.8% 84.0%
5025693 304.3.1.23 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › TiaS_FLD 0.58 42.0 4.71e-01 87.0% 97.9%
4132144 304.9.1.14 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF1743 0.58 42.0 4.69e-01 87.0% 97.9%
5044425 321.2.1.1 a+b two layers › Glutamine synthetase-like › C-terminal domain in urocanase › C-terminal domain in urocanase › Urocanase_C 0.57 46.0 3.84e-01 86.2% 68.8%
3419603 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.57 40.0 4.67e-01 78.9% 100.0%
4287252 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.56 45.0 4.05e-01 86.2% 62.3%
4574339 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.55 45.0 4.18e-01 86.2% 72.3%
4393513 304.60.1.8 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF27436 0.55 44.0 3.94e-01 86.2% 61.1%
4094763 304.60.1.8 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF27436 0.55 44.0 4.10e-01 86.2% 67.5%
4994518 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 0.55 50.0 4.39e-01 100.0% 88.1%
4510400 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 43.0 3.93e-01 86.2% 68.5%
3184299 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.53 45.0 4.47e-01 91.9% 98.5%
5054787 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.52 42.0 3.67e-01 86.2% 56.8%
5074951 304.111.1.1 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.52 46.0 4.08e-01 95.9% 95.6%
4238120 195.1.1.1 alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.52 37.0 3.16e-01 73.2% 95.2%
5052554 304.111.1.1 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.52 45.0 3.93e-01 95.9% 93.7%
4990703 304.111.1.1 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.51 46.0 3.96e-01 95.9% 90.8%
4954850 304.111.1.1 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.51 47.0 3.43e-01 100.0% 97.5%
4945623 304.111.1.0 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like 0.51 43.0 3.84e-01 93.5% 93.3%
4943288 304.103.1.1 a+b two layers › Alpha-beta plaits › FMN-dependent nitroreductase-like › FMN-dependent nitroreductase-like › Nitroreductase 0.50 43.0 3.62e-01 96.7% 87.5%
D5 medium residues 608-676_737-755
PDB