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putative_RNA-dependent_RNA_polymerase

Euk-Vir

Panax_notoginseng_virus_A

putative_RNA-dependent_RNA_polymerase__YP_009225665__Panax_notoginseng_virus_A__1777016

Identity

Accession:
YP_009225665 ↗
Protein ID:
putative_RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

88.6 mean pLDDT

Cluster

View cluster (56 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 14-92
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_009182195__Red_clover_powdery_mildew-associated_totivirus_7__1714368__D7-83
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.64 38.0 3.70e-01 72.2% 51.1%
4q63A00 2.40.10.430 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.63 43.0 4.10e-01 70.9% 66.7%
4g6iB01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.61 44.0 4.29e-01 82.3% 68.5%
1mbmA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.60 40.0 4.07e-01 83.5% 71.1%
4zgnB00 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 43.0 3.94e-01 75.9% 96.1%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 43.0 4.33e-01 98.7% 77.2%
3mlqH00 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.58 29.0 3.72e-01 91.1% 88.1%
3fanA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 37.0 3.85e-01 84.8% 69.9%
2kr7A02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.58 39.0 4.34e-01 82.3% 96.5%
4i1kA00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.58 39.0 3.49e-01 70.9% 54.2%
5gt8D02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.57 49.0 4.22e-01 93.7% 96.7%
2m89A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 38.0 3.24e-01 73.4% 90.3%
2cxiA03 3.30.56.10 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.54 37.0 3.86e-01 70.9% 81.4%
5tfmA01 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.54 41.0 3.86e-01 82.3% 88.8%
4frwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 40.0 3.83e-01 82.3% 87.5%
1vcaA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 39.0 3.80e-01 78.5% 83.1%
3qdhA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 38.0 3.09e-01 75.9% 56.4%
3zugB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.53 41.0 3.42e-01 83.5% 56.3%
3aqoA01 3.30.70.3400 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 38.0 3.82e-01 75.9% 98.8%
1mrzB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.52 36.0 3.29e-01 74.7% 50.9%
2c61A00 3.40.50.12240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 38.0 2.40e-01 77.2% 59.6%
2n01B00 2.60.40.2500 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.64e-01 84.8% 87.7%
2l8oA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 37.0 3.11e-01 78.5% 88.9%
3hrpA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.54e-01 78.5% 78.9%
2oz4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 3.30e-01 72.2% 76.3%
3pcoB04 3.30.56.10 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.50 35.0 3.62e-01 78.5% 77.3%
3fkuS02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 36.0 3.34e-01 75.9% 73.8%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5030523 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 43.0 4.14e-01 100.0% 65.3%
4609138 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.59 48.0 3.90e-01 88.6% 76.0%
4205165 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 42.0 4.15e-01 100.0% 72.9%
3804424 1.1.11.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › B3 0.58 39.0 3.46e-01 70.9% 53.3%
3822850 1.1.8.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.56 40.0 3.77e-01 75.9% 97.0%
3218202 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.55 42.0 3.65e-01 82.3% 91.1%
3786521 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.54 46.0 4.11e-01 96.2% 66.1%
5041753 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.54 37.0 3.35e-01 72.2% 79.1%
4242756 60.1.2.1 ↗ beta barrels › SPOC domain-like › SPOC domain-related › Ku70/80 subunit middle domain › Ku 0.54 39.0 2.98e-01 78.5% 35.7%
5036531 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 39.0 3.64e-01 77.2% 84.0%
4871762 223.1.1.12 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_2 0.54 36.0 3.14e-01 70.9% 78.0%
4943444 1.1.7.145 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › EFG_III 0.53 38.0 3.31e-01 77.2% 52.3%
3336210 1.1.11.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › DUF7271 0.53 39.0 3.76e-01 81.0% 68.9%
3939997 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.52 37.0 3.62e-01 77.2% 92.2%
4989577 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.52 39.0 3.38e-01 78.5% 73.3%
3452625 1.1.7.69 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.52 38.0 3.61e-01 96.2% 63.0%
3888845 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.52 38.0 3.60e-01 77.2% 73.7%
3409112 11.1.1.247 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › TIG_plexin 0.52 38.0 3.63e-01 78.5% 87.4%
3968427 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 38.0 3.17e-01 79.7% 74.0%
5075821 304.139.1.2 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › RAMPs 0.52 37.0 2.93e-01 78.5% 87.7%
3232689 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.51 39.0 3.76e-01 83.5% 90.5%
4016558 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.51 43.0 3.56e-01 94.9% 75.9%
3971124 223.1.1.58 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › 2CSK_N 0.51 39.0 3.48e-01 82.3% 87.8%
4295277 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 38.0 3.17e-01 82.3% 58.0%
4062716 304.17.1.1 ↗ a+b two layers › Alpha-beta plaits › N-utilization substance G protein NusG, N-terminal domain › N-utilization substance G protein NusG, N-terminal domain › NusG 0.50 37.0 3.36e-01 81.0% 86.7%
3667522 223.2.1.31 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_2 0.50 38.0 2.93e-01 81.0% 58.9%
5000537 2003.1.5.69 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GCD14 0.50 36.0 2.74e-01 75.9% 85.6%
D2 high residues 109-256_588-627
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009507835__Xanthophyllomyces_dendrorhous_virus_L1B__1167691__D135-271_599-614
D3 medium residues 257-273_290-398_441-500
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 44.7 1.30e-11 67.7% 22.1%
D4 medium residues 274-289_399-440_501-587
PDB
Domain cluster: rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 64.8 1.10e-17 60.0% 17.0%
D5 medium residues 641-759
PDB
Domain cluster: representative
D6 medium residues 760-822
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_009182174__Red_clover_powdery_mildew-associated_totivirus_1__1714362__D745-801