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RNA-dependent_RNA-polymerase

Euk-Vir

Pelargonium_ringspot_virus

RNA-dependent_RNA-polymerase__YP_009116639__Pelargonium_ringspot_virus__167020

Identity

Accession:
YP_009116639 ↗
Protein ID:
RNA-dependent_RNA-polymerase
Kingdom:
euk

Quality

78.1 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Tolucaviricetes› Tolivirales› Tombusviridae› Pelarspovirus› Pelargonium_ringspot_virus

TaxID: 167020

Cluster

View cluster (58 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 88-181
PDB
D2 high residues 619-732
PDB
Domain cluster: rep: P95_replicase__YP_009259667__Pelargonium_leaf_curl_virus__35280__D527-559_693-852
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 85.8 4.10e-24 100.0% 24.3%
D3 medium residues 219-236_238-401_415-432
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337688__Beihai_tombus-like_virus_7__1922728__D528-588_642-697_774-796
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 112.3 3.60e-32 81.0% 35.0%
D4 medium residues 402-414_473-529
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337657__Changjiang_tombus-like_virus_11__1922804__D27-99
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 69.1 4.60e-19 84.3% 11.7%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.73 63.0 4.79e-01 100.0% 58.5%
3aa0B01 1.20.58.570 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › F-actin capping protein, alpha/beta subunit, N-terminal domain 0.66 34.0 3.18e-01 70.0% 38.6%
2pw9A01 4.10.80.30 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › DNA polymerase; domain 6 0.57 25.0 3.25e-01 70.0% 96.0%
2wpvE00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 38.0 2.58e-01 71.4% 18.2%
6l2cB00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.56 45.0 2.91e-01 94.3% 83.0%
4uwmA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.54 44.0 2.80e-01 91.4% 30.4%
6tmfI00 1.10.455.10 Mainly Alpha › Orthogonal Bundle › Ribosomal Protein S7 › Ribosomal protein S7/S5 0.53 38.0 2.85e-01 80.0% 64.0%
2cpmA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.53 28.0 2.56e-01 71.4% 35.1%
6vq6H01 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 37.0 2.77e-01 77.1% 52.0%
3lrtA02 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 40.0 3.28e-01 87.1% 95.5%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3364208 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.68 36.0 2.24e-01 71.4% 9.4%
3998693 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.65 50.0 3.14e-01 85.7% 88.9%
4966410 3281.1.1.0 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related 0.63 46.0 2.71e-01 78.6% 28.1%
141070 223.3.1.1 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase 0.62 32.0 3.51e-01 71.4% 57.9%
5055279 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.55 37.0 2.78e-01 71.4% 86.3%
1278602 223.3.1.1 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase 0.55 31.0 3.28e-01 71.4% 61.7%
3666479 109.4.1.1156 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › E_motif 0.54 38.0 2.97e-01 72.9% 79.4%
3303026 109.4.1.1254 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.54 37.0 2.26e-01 71.4% 11.4%
3578140 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.54 39.0 2.48e-01 78.6% 59.5%
3585734 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.54 38.0 3.17e-01 80.0% 62.0%
5000862 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.53 40.0 2.78e-01 82.9% 71.1%
3494392 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.53 39.0 2.48e-01 78.6% 60.0%
4936754 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.52 39.0 3.30e-01 81.4% 80.8%
3512028 5001.1.1.5 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_3 0.52 38.0 2.66e-01 81.4% 84.4%
3580607 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 28.0 3.21e-01 90.0% 73.3%
3641285 109.4.1.1254 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.51 37.0 2.22e-01 78.6% 46.3%
3325708 109.4.1.1254 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.51 37.0 2.51e-01 77.1% 83.3%
D5 medium residues 433-472_530-618
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337274__Changjiang_tombus-like_virus_14__1922807__D158-196_253-344
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 101.0 9.70e-29 69.0% 18.3%
PF00998.29 RdRP_3 51.1 1.30e-13 31.0% 8.2%