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RdRp

Euk-Vir

Sanxia_permutotetra-like_virus_1

RdRp__YP_009337650__Sanxia_permutotetra-like_virus_1__1923365

Identity

Accession:
YP_009337650 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

77.4 mean pLDDT

Cluster

View cluster (20 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 76-113_148-281_398-434
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
PF22152.2 best Permu_RdRp_palm 188.6 2.00e-55 62.7% 36.4%
PF22152.2 Permu_RdRp_palm 38.1 1.20e-09 18.2% 10.6%
D2 high residues 778-929
PDB
D3 medium residues 282-397_435-494
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D328-384_485-539
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 155.0 3.50e-45 66.5% 31.6%
PF22152.2 Permu_RdRp_palm 79.3 3.60e-22 35.2% 16.5%
D4 medium residues 495-548
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vwxT01 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.68 49.0 4.00e-01 75.9% 58.8%
1ko2A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.62 47.0 3.16e-01 85.2% 42.2%
2hqlA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 43.0 3.72e-01 75.9% 90.1%
2el8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 43.0 3.73e-01 79.6% 68.1%
2cqaA01 2.40.50.360 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain 0.60 40.0 3.64e-01 70.4% 59.5%
3h6qA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.59 42.0 3.02e-01 75.9% 88.1%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.58 41.0 2.90e-01 74.1% 27.9%
3a57A00 2.60.270.30 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › Vibrio parahaemolyticus thermostable direct hemolysin 0.57 38.0 2.87e-01 70.4% 57.8%
6xw5A01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.57 43.0 3.14e-01 87.0% 77.5%
3htyA00 2.40.128.280 Mainly Beta › Beta Barrel › Lipocalin › 0.57 42.0 3.57e-01 81.5% 64.9%
4ebrA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.57 45.0 3.28e-01 88.9% 40.1%
2qlvB02 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.56 36.0 4.06e-01 75.9% 94.7%
3sc7X01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.56 40.0 2.52e-01 77.8% 13.1%
3p0cA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.56 42.0 3.31e-01 79.6% 51.4%
4fg9A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.56 41.0 3.64e-01 79.6% 73.4%
8f5pE01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 38.0 2.34e-01 74.1% 39.2%
8b4hA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.55 37.0 2.78e-01 72.2% 100.0%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.55 42.0 3.21e-01 88.9% 66.2%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.55 44.0 3.54e-01 100.0% 77.9%
4c92C00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.55 37.0 3.33e-01 70.4% 64.6%
3s95A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 39.0 3.35e-01 88.9% 45.5%
1v1qA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 38.0 3.13e-01 75.9% 47.3%
3vwoA02 2.10.70.40 Mainly Beta › Ribbon › Complement Module; domain 1 › peptidoglycan hydrolase 0.55 37.0 3.87e-01 72.2% 98.0%
2qrdB01 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.55 35.0 3.85e-01 77.8% 91.9%
4oc8A02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.54 42.0 3.07e-01 90.7% 44.8%
3k0yA02 2.60.40.2370 Mainly Beta › Sandwich › Immunoglobulin-like › NigD-like, C-terminal beta sandwich domain 0.54 40.0 3.09e-01 83.3% 80.5%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.53 42.0 3.63e-01 98.1% 54.4%
1olrA00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.52 40.0 2.81e-01 92.6% 34.5%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.52 40.0 3.02e-01 87.0% 83.2%
5lddC00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 40.0 2.94e-01 88.9% 41.7%
2fdoA00 3.30.1970.10 Alpha Beta › 2-Layer Sandwich › AF2331-like fold › AF2331-like 0.52 33.0 2.83e-01 74.1% 36.6%
1uyjA01 3.30.360.60 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › 0.52 37.0 3.37e-01 88.9% 52.4%
1zc0A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 41.0 2.67e-01 94.4% 41.3%
3vl9B00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.52 40.0 2.81e-01 94.4% 33.9%
1kyfA01 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.52 36.0 2.83e-01 75.9% 64.2%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.52 35.0 3.20e-01 77.8% 50.0%
2v8qB00 6.20.250.60 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.52 36.0 3.34e-01 74.1% 64.4%
1jeyB02 2.40.290.10 Mainly Beta › Beta Barrel › Ku70; Chain: A; Domain 2 › 0.50 37.0 2.63e-01 85.2% 91.0%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4632710 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.77 48.0 5.23e-01 72.2% 77.8%
3888254 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 47.0 5.01e-01 72.2% 77.8%
3742185 2003.1.5.26 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_28 0.65 44.0 2.62e-01 70.4% 57.5%
4990017 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.65 54.0 3.85e-01 96.3% 68.8%
1829536 6173.1.1.0 ↗ beta barrels › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 0.63 42.0 4.38e-01 70.4% 84.3%
4606349 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 44.0 3.70e-01 75.9% 65.3%
4203291 3256.1.1.2 ↗ a+b two layers › DUF2233 N-terminal domain › DUF2233 N-terminal domain › DUF2233 N-terminal domain › eIF3g 0.61 40.0 4.55e-01 87.0% 100.0%
3288884 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.61 46.0 3.78e-01 85.2% 63.8%
4954981 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.60 49.0 3.54e-01 96.3% 68.8%
3173378 109.4.1.338 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIC1 0.59 48.0 3.23e-01 96.3% 59.2%
3593482 2.1.1.135 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF3592 0.59 43.0 3.52e-01 77.8% 61.0%
3303657 2.1.1.284 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › CDC24_OB3, CDC24_OB1 0.57 40.0 2.74e-01 79.6% 19.5%
4003540 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.57 41.0 2.41e-01 81.5% 28.2%
4594994 394.1.1.0 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins 0.57 41.0 3.73e-01 79.6% 62.8%
4041984 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.56 38.0 4.07e-01 74.1% 84.4%
4956007 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.56 36.0 3.01e-01 72.2% 34.3%
3896484 220.1.1.7 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.56 38.0 2.98e-01 70.4% 34.2%
3572060 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.55 40.0 3.15e-01 77.8% 54.2%
3684495 136.1.1.1 ↗ alpha complex topology › Heme-dependent peroxidases › Heme-dependent peroxidases › Heme-dependent peroxidases › peroxidase 0.55 42.0 2.71e-01 85.2% 38.6%
5030187 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.55 37.0 3.39e-01 72.2% 91.0%
4188650 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.54 36.0 3.00e-01 75.9% 35.2%
4120506 243.11.1.4 ↗ a+b two layers › Cystatin-like › NP_346341.1 protein › NP_346341.1 protein › PF29632 0.53 37.0 3.37e-01 75.9% 72.5%
1125751 4086.1.1.1 ↗ a+b two layers › AMPKBI-like › AMPKBI-like › AMPKBI-like › AMPKBI 0.53 37.0 3.25e-01 74.1% 64.8%
4477850 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.53 34.0 2.90e-01 72.2% 35.0%
4483987 374.1.1.2 ↗ few secondary structure elements › HIPIP (high potential iron protein) › HIPIP (high potential iron protein) › HIPIP (high potential iron protein) › BssC_TutF 0.53 36.0 3.67e-01 74.1% 76.4%
4982249 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.52 36.0 3.11e-01 87.0% 43.2%
145216 4086.1.1.1 ↗ a+b two layers › AMPKBI-like › AMPKBI-like › AMPKBI-like › AMPKBI 0.51 35.0 2.99e-01 74.1% 59.6%
3509056 221.13.1.0 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain 0.51 37.0 2.96e-01 81.5% 82.4%
4976982 330.6.1.0 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain 0.51 36.0 2.93e-01 75.9% 55.5%
4403166 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.51 34.0 3.32e-01 72.2% 81.5%
5008812 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.51 39.0 3.22e-01 88.9% 44.8%
5077468 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.50 38.0 2.63e-01 85.2% 80.9%
3721942 4086.1.1.1 ↗ a+b two layers › AMPKBI-like › AMPKBI-like › AMPKBI-like › AMPKBI 0.50 37.0 3.06e-01 81.5% 56.2%
3175033 4086.1.1.1 ↗ a+b two layers › AMPKBI-like › AMPKBI-like › AMPKBI-like › AMPKBI 0.50 37.0 3.20e-01 81.5% 73.3%
D5 medium residues 549-678
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D29-60_540-665
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22260.2 best Permu_RdRp_thumb 122.9 7.90e-36 69.2% 86.4%