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RNA_dependent_RNA_polymerase

Euk-Vir

Arhar_cryptic_virus-I_Viruses.

RNA_dependent_RNA_polymerase__YP_009026407__Arhar_cryptic_virus-I_Viruses.__X

Identity

Accession:
YP_009026407 ↗
Protein ID:
RNA_dependent_RNA_polymerase
Kingdom:
euk

Quality

93.7 mean pLDDT

Cluster

View cluster (450 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 33-57_394-465
PDB
Domain cluster: rep: putative_RNA_dependent_RNA_polymerse__YP_001686783__Raphanus_sativus_cryptic_virus_2__351495__D398-472
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 28.8 7.70e-07 59.8% 12.7%
D2 medium residues 58-78_107-210_258-302
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
PF00680.26 best RdRP_1 88.3 6.60e-25 72.9% 26.2%
PF00680.26 RdRP_1 33.4 3.10e-08 28.2% 10.2%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4bbyA05 3.30.300.330 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.53 25.0 3.03e-01 100.0% 65.7%
2fq3A00 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 27.0 3.61e-01 71.8% 100.0%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.50 29.0 3.39e-01 79.4% 83.8%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1699894 304.48.2.2 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Permu_RdRp_palm 0.83 79.0 5.41e-01 100.0% 69.5%
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 0.79 75.0 5.57e-01 100.0% 65.3%
3878013 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 67.0 5.02e-01 100.0% 66.5%
3254023 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 55.0 5.17e-01 82.4% 91.7%
4071235 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 56.0 3.91e-01 87.6% 35.6%
3976334 4995.1.1.3 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › MlrA_helical 0.59 30.0 4.06e-01 78.2% 95.3%
3483524 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 0.56 52.0 4.25e-01 100.0% 66.6%
D3 medium residues 79-106_211-257_303-385
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 86.9 1.80e-24 53.2% 21.1%
PF00680.26 RdRP_1 46.8 2.50e-12 38.0% 11.3%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.85 61.0 7.10e-01 77.8% 100.0%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.83 55.0 6.73e-01 75.3% 100.0%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.82 61.0 6.51e-01 82.3% 85.8%
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.82 61.0 6.90e-01 82.3% 99.2%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.81 61.0 6.44e-01 82.3% 85.9%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.78 56.0 6.53e-01 77.8% 100.0%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.77 61.0 6.69e-01 81.0% 98.5%
4hkqA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.68 47.0 4.94e-01 84.8% 77.1%
7uinD01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.67 57.0 5.62e-01 90.5% 91.6%
6dgiA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.66 24.0 3.52e-01 81.0% 73.5%
1hi8A03 3.30.70.1600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 54.0 5.22e-01 89.9% 92.6%
2efpA02 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 34.0 4.21e-01 70.9% 92.9%
3hvwA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.58 45.0 4.52e-01 81.0% 84.9%
6eibD00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.56 46.0 4.67e-01 92.4% 87.2%
5o60I00 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.55 39.0 4.28e-01 76.6% 90.5%
4v19J00 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.55 38.0 3.73e-01 77.2% 65.5%
3tviA02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.55 38.0 3.83e-01 70.9% 73.0%
1s5jA03 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.53 44.0 4.51e-01 89.9% 97.5%
1zavA01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.52 39.0 4.16e-01 77.8% 91.1%
3a1yG01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.52 40.0 4.30e-01 80.4% 94.8%
1sz7A00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.52 35.0 3.53e-01 100.0% 67.3%
4hubG01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.51 35.0 3.43e-01 76.6% 63.2%
2kloA00 1.10.10.1420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DNA replication factor Cdt1, C-terminal WH domain 0.50 25.0 2.64e-01 81.0% 52.2%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1875037 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 76.0 5.57e-01 94.3% 80.8%
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 0.84 80.0 5.95e-01 100.0% 84.9%
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 0.70 58.0 4.38e-01 86.7% 54.1%
3939861 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 48.0 5.41e-01 81.6% 92.5%
3983816 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 0.69 60.0 5.08e-01 91.8% 73.6%
3173834 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 0.69 58.0 4.27e-01 89.9% 80.5%
4872037 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 59.0 4.89e-01 91.8% 97.7%
3068775 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 55.0 5.02e-01 86.1% 80.3%
3916504 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 51.0 4.30e-01 79.1% 89.4%
4434853 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 4.73e-01 86.7% 95.8%
4890630 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 53.0 4.61e-01 84.8% 70.3%
3630469 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 0.66 56.0 4.44e-01 91.8% 75.1%
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 0.63 52.0 4.03e-01 89.2% 72.5%
3170846 304.60.1.12 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › PF29803 0.62 47.0 4.27e-01 77.8% 93.8%
3947798 304.8.1.70 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Phage_GPA 0.61 46.0 3.81e-01 79.1% 55.4%
3787148 304.48.1.37 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_2 0.60 48.0 4.14e-01 84.8% 63.7%
3939178 304.48.1.37 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_2 0.59 47.0 4.50e-01 84.2% 83.2%
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 0.59 52.0 4.15e-01 96.2% 93.8%
3938275 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 47.0 4.02e-01 84.8% 53.7%
3984781 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 46.0 4.65e-01 84.8% 88.7%
3286133 304.48.1.14 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF 0.57 47.0 4.72e-01 88.0% 88.1%
4101583 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.56 40.0 4.00e-01 77.8% 69.7%
3410191 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.56 39.0 3.53e-01 76.6% 52.1%
4941744 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.56 39.0 3.66e-01 77.2% 56.5%
4322200 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.55 39.0 3.87e-01 76.6% 67.6%
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 39.0 3.74e-01 77.8% 62.8%
4149886 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.55 39.0 3.86e-01 76.6% 67.6%
3571315 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 0.55 50.0 4.40e-01 100.0% 95.3%
4287252 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.55 39.0 3.79e-01 76.6% 65.7%
4445437 304.60.1.8 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF27436 0.55 38.0 3.76e-01 76.6% 65.1%
4959966 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 37.0 3.51e-01 76.6% 56.9%
4666950 304.60.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like 0.54 38.0 3.79e-01 77.2% 67.6%
4574339 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 39.0 3.93e-01 81.0% 74.2%
5080034 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 39.0 3.60e-01 77.2% 58.5%
4927452 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 39.0 3.55e-01 81.0% 57.1%
5000842 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 39.0 3.46e-01 77.2% 53.2%
4027875 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.54 40.0 3.86e-01 77.8% 68.3%
4050881 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.53 39.0 3.39e-01 77.8% 49.8%
4990626 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.53 37.0 3.41e-01 77.8% 56.0%
5070514 4954.1.1.1 ↗ a+b complex topology › central helical domain in RNA-polymerase beta-prime subunit › central helical domain in RNA-polymerase beta-prime subunit › central helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 0.53 37.0 3.19e-01 72.8% 48.8%
3313630 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.52 38.0 3.47e-01 77.2% 58.1%
3787075 304.60.1.10 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF28227 0.52 38.0 3.61e-01 76.6% 67.9%
3630321 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.51 39.0 4.11e-01 82.3% 86.9%
3275810 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.51 37.0 3.63e-01 80.4% 68.2%
3695357 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.51 39.0 4.10e-01 83.5% 86.9%
3613370 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.51 37.0 3.95e-01 77.2% 86.7%
5037904 304.48.1.31 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Cas10-Cmr2_palm2 0.51 42.0 3.72e-01 89.9% 78.7%
3482305 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.50 39.0 3.92e-01 82.9% 78.2%
4074141 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.50 40.0 4.04e-01 82.3% 83.9%