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RNA-dependent_RNA_polymerase

Euk-Vir

Beihai_shrimp_virus_6

RNA-dependent_RNA_polymerase__YP_009333611__Beihai_shrimp_virus_6__1922672

Identity

Accession:
YP_009333611 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.4 mean pLDDT

Cluster

View cluster (17 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 14-57
PDB
D2 high residues 63-270
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337879__Hubei_noda-like_virus_9__1922989__D136-259_287-345
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19222.6 best Noda_Vmethyltr 184.1 1.70e-54 70.7% 98.0%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1nkvB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 45.0 4.34e-01 80.3% 96.1%
3f8tA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 20.0 3.22e-01 75.5% 87.5%
3lidA03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 26.0 3.53e-01 90.4% 91.7%
2qrdA00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.53 25.0 3.29e-01 90.4% 78.9%
1c8uA02 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.51 24.0 3.16e-01 85.1% 79.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3242625 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.61 23.0 3.16e-01 87.5% 64.5%
3956757 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 28.0 4.04e-01 90.9% 97.9%
4295277 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.54 26.0 3.03e-01 91.8% 60.0%
5060936 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.53 19.0 2.79e-01 74.5% 68.9%
4269575 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.52 32.0 3.62e-01 76.4% 79.4%
4399650 223.1.1.59 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › ArlS_N 0.51 29.0 3.09e-01 91.8% 60.6%
3965912 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 22.0 3.18e-01 91.3% 86.3%
5021202 223.1.1.97 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › sCache_2 0.51 31.0 3.83e-01 90.4% 94.1%
4076860 7512.1.1.16 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Capsule_synth 0.51 33.0 2.34e-01 88.5% 20.9%
D3 high residues 722-840
PDB
Domain cluster: rep: hypothetical_protein__YP_009337806__Shuangao_insect_virus_11__1923467__D743-868
D4 medium residues 271-362
PDB
Domain cluster: rep: hypothetical_protein__YP_009336769__Hubei_diptera_virus_16__1922877__D264-353
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4huqS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.66 47.0 3.88e-01 87.0% 41.5%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.64 37.0 4.10e-01 94.6% 73.2%
2k7iA01 3.30.160.160 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YegP-like 0.61 33.0 4.29e-01 92.4% 100.0%
2l2mA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 32.0 3.64e-01 84.8% 68.6%
4p78C00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.59 38.0 4.27e-01 95.7% 89.4%
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.59 49.0 4.55e-01 91.3% 88.1%
1e8oD00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.59 33.0 3.56e-01 93.5% 63.2%
7pluA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 45.0 4.22e-01 85.9% 100.0%
4rbnA01 3.10.450.330 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 40.0 3.60e-01 73.9% 82.9%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.56 42.0 3.80e-01 79.3% 92.1%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.56 38.0 3.99e-01 81.5% 78.3%
3lxrF00 1.10.4120.20 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › 0.54 44.0 3.58e-01 91.3% 85.6%
4za3A01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.54 39.0 3.30e-01 78.3% 78.5%
2oztA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 39.0 3.63e-01 80.4% 78.0%
3h5kA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.51 38.0 3.09e-01 78.3% 92.1%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.51 34.0 3.71e-01 90.2% 82.3%
2hdwA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 42.0 3.21e-01 94.6% 54.8%
3bwxA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 44.0 3.13e-01 98.9% 46.0%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3400005 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.74 34.0 4.18e-01 85.9% 68.3%
3388887 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.69 34.0 4.01e-01 89.1% 67.7%
3987799 4221.1.1.1 ↗ a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like › DUF1797 0.66 38.0 4.25e-01 93.5% 74.3%
3286911 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.65 44.0 4.94e-01 78.3% 92.9%
7726 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.62 38.0 4.59e-01 76.1% 100.0%
3925471 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.61 30.0 3.60e-01 89.1% 70.0%
3509389 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.61 38.0 3.43e-01 77.2% 44.6%
3606532 2484.6.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Periplasmic domain of ExbD/TolR › Periplasmic domain of ExbD/TolR 0.57 33.0 3.35e-01 93.5% 55.6%
3933827 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.57 33.0 2.66e-01 94.6% 27.9%
3478366 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 43.0 4.14e-01 80.4% 95.2%
3649062 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.56 47.0 4.03e-01 94.6% 92.3%
3737796 101.1.1.10 ↗ alpha arrays › HTH › HTH › Three-helical HTH › ARID 0.56 45.0 4.63e-01 96.7% 91.1%
3284714 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.56 35.0 4.09e-01 72.8% 93.7%
3798524 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.55 43.0 4.05e-01 84.8% 93.0%
4989502 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.54 43.0 2.80e-01 96.7% 18.4%
3652426 206.1.1.74 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, PK_Tyr_Ser-Thr 0.54 43.0 2.95e-01 89.1% 55.5%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.54 35.0 3.56e-01 85.9% 67.8%
4959885 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.53 36.0 3.78e-01 88.0% 76.5%
4998603 4312.1.1.0 ↗ a+b two layers › RelE-like › RelE-like › RelE-like 0.53 35.0 3.82e-01 94.6% 84.0%
3904569 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.52 41.0 3.70e-01 83.7% 89.6%
3907024 260.1.1.1 ↗ a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.52 33.0 2.29e-01 89.1% 17.8%
3407532 4.1.1.326 ↗ beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.52 28.0 3.61e-01 84.8% 96.0%
4478350 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.52 43.0 3.97e-01 93.5% 93.3%
3364428 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.52 40.0 3.08e-01 84.8% 44.1%
5072644 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.51 42.0 3.85e-01 93.5% 91.5%
3231587 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 37.0 3.79e-01 92.4% 81.1%
3621979 3198.1.1.1 ↗ alpha bundles › ABA-1 repeat unit › ABA-1 repeat unit › ABA-1 repeat unit › NPA 0.50 44.0 4.10e-01 100.0% 100.0%
3964724 3675.1.1.1 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.50 39.0 3.36e-01 84.8% 56.1%
4026643 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.50 36.0 3.77e-01 97.8% 82.4%
D5 medium residues 403-540_577-633
PDB
Domain cluster: rep: hypothetical_protein__YP_009336545__Beihai_sphaeromadae_virus_2__1922708__D440-558_579-635
D6 medium residues 541-576_634-721
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181