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RdRP_2

Euk-Vir

Citrus_leprosis_virus_C2

RdRP_2__YP_009509062__Citrus_leprosis_virus_C2__2052685

Identity

Accession:
YP_009509062 ↗
Protein ID:
RdRP_2
Kingdom:
euk

Quality

87.1 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Kitaviridae› Cilevirus› Citrus_leprosis_virus_C2

TaxID: 2052685

Cluster

View cluster (85 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 350-439
PDB
Domain cluster: rep: RdRp__YP_009388601__Aedes_camptorhynchus_negev-like_virus_Viruses.__X__D397-476
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 42.3 6.70e-11 100.0% 20.0%
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6t0bf00 1.25.40.40 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI 0.64 37.0 3.63e-01 86.7% 50.0%
2wglA00 1.10.4190.10 Mainly Alpha › Orthogonal Bundle › Urease accessory protein UreF › Urease accessory protein UreF 0.61 47.0 3.60e-01 82.2% 69.9%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.60 44.0 4.29e-01 85.6% 71.1%
1khvA05 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.59 47.0 4.64e-01 100.0% 81.4%
1uurA01 1.20.58.240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › STAT; domain 1 0.57 50.0 4.74e-01 97.8% 94.5%
3c8zA02 1.20.120.640 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.57 36.0 3.78e-01 85.6% 68.7%
3e3vA03 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 0.57 32.0 3.87e-01 74.4% 87.5%
2jucA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.57 32.0 3.86e-01 73.3% 89.1%
1yowA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.56 47.0 3.56e-01 93.3% 87.8%
5ulcX00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.56 40.0 3.62e-01 74.4% 93.4%
2dodA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.56 34.0 3.58e-01 82.2% 67.1%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.55 34.0 3.50e-01 97.8% 64.3%
1v4aA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.55 38.0 3.22e-01 71.1% 100.0%
3edvA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 48.0 3.82e-01 95.6% 54.6%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.55 38.0 3.74e-01 83.3% 65.7%
1xwmA00 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.55 44.0 3.37e-01 87.8% 40.1%
3lbxB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 47.0 4.45e-01 96.7% 92.5%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 47.0 4.54e-01 96.7% 96.1%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.54 45.0 4.09e-01 98.9% 66.7%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 47.0 4.56e-01 97.8% 94.1%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 39.0 4.13e-01 100.0% 90.7%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.54 46.0 4.75e-01 100.0% 100.0%
4cybD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 45.0 3.73e-01 94.4% 83.0%
1xl3C00 1.20.1280.80 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.53 41.0 4.14e-01 85.6% 82.4%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 45.0 4.01e-01 96.7% 72.1%
3x29A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.52 45.0 3.78e-01 100.0% 89.2%
1n1fA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.52 40.0 3.39e-01 82.2% 73.2%
1oqcA00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.52 38.0 3.56e-01 97.8% 62.5%
3kbtA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 45.0 3.24e-01 100.0% 52.1%
3u61D03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.51 40.0 4.00e-01 83.3% 84.6%
4ga4A01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.51 31.0 3.47e-01 90.0% 80.6%
2f33A03 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 32.0 3.24e-01 92.2% 63.2%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 44.0 4.20e-01 96.7% 90.6%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.51 38.0 4.12e-01 96.7% 100.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4026902 109.4.1.22 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N 0.63 40.0 3.42e-01 100.0% 39.3%
5041952 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.60 53.0 4.68e-01 98.9% 88.1%
3499494 109.4.1.522 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RPAP1_C 0.59 51.0 3.10e-01 98.9% 19.1%
3795 603.2.1.2 ↗ alpha bundles › STAT-like › STAT › STAT › Dict-STAT-coil 0.57 50.0 4.63e-01 97.8% 88.1%
3580914 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.57 38.0 3.92e-01 85.6% 71.8%
3484031 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 49.0 4.32e-01 96.7% 74.8%
3624929 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 46.0 4.19e-01 90.0% 71.2%
3756535 604.1.1.5 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_3 0.56 48.0 4.49e-01 96.7% 82.6%
3473142 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.55 48.0 4.20e-01 98.9% 77.1%
3570499 604.1.1.95 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › KIAA1755_C 0.55 46.0 4.61e-01 95.6% 92.6%
3655114 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 42.0 3.68e-01 98.9% 54.3%
3757581 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.54 47.0 4.46e-01 96.7% 90.5%
3900921 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.54 46.0 4.22e-01 96.7% 81.7%
3883670 604.1.1.7 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › SR_plectin_7 0.53 45.0 4.19e-01 96.7% 86.7%
3894879 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.53 46.0 4.43e-01 98.9% 94.3%
3489764 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.53 46.0 4.43e-01 97.8% 94.3%
3603904 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 0.53 36.0 3.61e-01 98.9% 68.9%
3855973 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.53 45.0 4.45e-01 97.8% 96.0%
3260134 622.4.1.61 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Mit_KHE1 0.53 40.0 3.53e-01 84.4% 74.5%
3570651 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.52 45.0 4.47e-01 97.8% 97.9%
3828970 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.52 45.0 4.46e-01 96.7% 92.6%
3704342 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 44.0 3.11e-01 100.0% 76.4%
3841673 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.52 43.0 4.24e-01 96.7% 98.0%
3705783 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.51 38.0 3.88e-01 82.2% 96.7%
5016525 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.51 34.0 3.55e-01 93.3% 76.2%
4877620 604.13.1.1 ↗ alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like › USP8_dimer 0.50 42.0 3.82e-01 96.7% 69.3%
3484674 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 44.0 3.66e-01 100.0% 91.5%
D2 medium residues 1-61_123-154_255-272
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 30.8 2.00e-07 60.4% 14.5%
D3 medium residues 62-122_155-178_224-254
PDB
Domain cluster: rep: RdRp__YP_009388601__Aedes_camptorhynchus_negev-like_virus_Viruses.__X__D86-108_120-151_186-211_254-279
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3oa3A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.50 34.0 2.71e-01 70.7% 81.8%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4958228 601.23.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III 0.52 37.0 2.66e-01 73.3% 71.7%
3833310 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.50 26.0 2.80e-01 97.4% 57.0%
D4 medium residues 179-223_273-349
PDB
Domain cluster: rep: hypothetical_protein__YP_009337242__Hubei_virga-like_virus_11__1923326__D790-809_821-831_888-944
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 68.3 8.50e-19 63.1% 17.1%