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RNA-dependent_RNA_polymerase

Euk-Vir

Wenzhou_narna-like_virus_2

RNA-dependent_RNA_polymerase__YP_009336518__Wenzhou_narna-like_virus_2__1923577

Identity

Accession:
YP_009336518 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

72.3 mean pLDDT

Cluster

View cluster (39 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 46-182
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337264__Wenling_narna-like_virus_1__1923501__D1-107
D2 medium residues 183-241
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7xb6B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 40.0 2.81e-01 72.9% 70.8%
4n06A02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.55 39.0 2.61e-01 76.3% 76.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4433034 1137.1.1.0 ↗ a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain 0.54 37.0 3.19e-01 71.2% 87.8%
3965667 109.4.1.520 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HemY_N 0.53 43.0 2.66e-01 94.9% 42.2%
5033515 2004.1.1.97 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MobB 0.51 39.0 2.77e-01 83.1% 29.5%
D3 medium residues 242-278_298-317
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4griA05 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.54 45.0 3.83e-01 94.7% 73.2%
D4 medium residues 318-359_395-457
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qq6A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 41.0 3.97e-01 81.0% 79.3%
2inbA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.53 39.0 3.65e-01 77.1% 99.2%
1uqtA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 41.0 3.12e-01 100.0% 35.8%
7dg2C01 1.10.10.1200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › MAGE homology domain, winged helix WH1 motif 0.50 31.0 3.44e-01 82.9% 81.3%
3dxpA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.50 37.0 2.89e-01 77.1% 69.1%
3vw4A01 1.10.340.50 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › 0.50 32.0 3.39e-01 75.2% 72.8%
1j09A05 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.50 42.0 4.30e-01 100.0% 99.0%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3983816 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.76 69.0 5.19e-01 100.0% 54.8%
None — 0.75 68.0 4.68e-01 100.0% 42.8%
3258406 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.74 68.0 4.20e-01 100.0% 27.1%
3789227 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.73 66.0 4.71e-01 100.0% 50.3%
3454701 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.73 67.0 4.86e-01 100.0% 54.3%
4424453 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.72 65.0 4.09e-01 100.0% 28.0%
3382764 626.1.1.0 ↗ alpha complex topology › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) 0.72 65.0 3.94e-01 100.0% 21.7%
3911488 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.70 60.0 4.42e-01 93.3% 53.5%
3238428 181.1.1.0 ↗ 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 0.59 38.0 4.32e-01 72.4% 86.3%
3907339 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.56 50.0 3.82e-01 100.0% 47.8%
3823296 2003.1.2.9 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GDI 0.56 47.0 3.01e-01 94.3% 72.1%
5044192 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.55 39.0 2.59e-01 73.3% 32.0%
5027420 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.54 40.0 2.80e-01 78.1% 35.5%
3933890 101.1.1.76 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 0.53 32.0 3.31e-01 88.6% 62.0%
5019219 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.51 40.0 2.96e-01 85.7% 62.7%
3929463 198.1.1.4 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › DUF3456 0.51 37.0 3.33e-01 76.2% 86.9%
4275897 101.8.1.2 ↗ alpha arrays › HTH › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › Anticodon_2 0.50 42.0 3.64e-01 99.0% 58.2%
D5 medium residues 360-394_458-562
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588
D6 medium residues 563-593_648-712
PDB
D7 medium residues 594-647
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ev6A03 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.75 61.0 6.03e-01 90.7% 100.0%
1h6vA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.73 64.0 4.17e-01 100.0% 48.3%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.71 59.0 5.22e-01 100.0% 64.7%
4ke2A00 6.10.140.1860 Special › Helix non-globular › Helix Hairpins › 0.70 60.0 4.14e-01 100.0% 76.5%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.70 58.0 5.78e-01 94.4% 87.7%
7toiA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.65 56.0 3.71e-01 94.4% 57.2%
3d5lA03 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 0.64 45.0 4.57e-01 75.9% 78.8%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 52.0 4.72e-01 100.0% 67.9%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.62 52.0 4.75e-01 100.0% 71.6%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.62 52.0 4.93e-01 100.0% 80.9%
3eslA01 1.20.58.2070 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 49.0 4.44e-01 94.4% 64.0%
3fhnA02 1.20.58.1420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain B 0.60 52.0 4.12e-01 100.0% 59.8%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.60 48.0 4.06e-01 88.9% 53.8%
4r3aA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.59 48.0 3.50e-01 100.0% 30.7%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.58 47.0 4.32e-01 98.1% 98.7%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.58 51.0 3.71e-01 100.0% 64.1%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.57 43.0 4.05e-01 88.9% 67.7%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 45.0 3.95e-01 100.0% 80.2%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3904078 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.75 64.0 5.89e-01 100.0% 82.2%
3690468 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 61.0 3.88e-01 94.4% 21.2%
3785926 101.1.15.3 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain › HAT1_C_fung 0.70 61.0 4.83e-01 100.0% 91.3%
3633232 616.1.1.1 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.69 59.0 3.95e-01 100.0% 24.8%
3180974 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.69 59.0 5.87e-01 100.0% 96.4%
3846955 198.1.1.10 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2, SapB_1, Saposin 0.67 57.0 5.05e-01 98.1% 66.3%
3976663 3812.1.1.1 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › T3SS_needle_E 0.63 53.0 5.05e-01 94.4% 89.2%
5043119 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.61 52.0 4.80e-01 94.4% 74.3%
3539986 5058.1.1.90 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › TMEM169 0.61 50.0 4.63e-01 98.1% 98.7%
4865215 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.60 48.0 4.80e-01 87.0% 90.7%
3554931 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.60 48.0 4.89e-01 88.9% 90.7%
3973453 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.58 49.0 4.39e-01 100.0% 83.7%
1948638 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.58 46.0 4.68e-01 87.0% 90.7%
5055477 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.56 48.0 4.24e-01 98.1% 90.0%
5048061 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.55 48.0 4.79e-01 100.0% 98.2%
3582775 109.4.1.46 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IBN_N 0.55 42.0 2.68e-01 87.0% 15.4%
D8 medium residues 773-826
PDB