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RNA-dependent_RNA_polymerase

Euk-Vir

Vanilla_latent_virus

RNA-dependent_RNA_polymerase__YP_009389473__Vanilla_latent_virus__2016426

Identity

Accession:: YP_009389473 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

75.6 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Alphaflexiviridae› Allexivirus› Vanilla_latent_virus

TaxID: 2016426

Cluster

View cluster (13 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 288-366

PDB

Domain cluster: rep: replicase_protein__YP_001655010__Phaius_virus_X__457382__D294-350

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01660.23 best	Vmethyltransf	27.8	1.80e-06	65.8%	16.4%

CATH (33)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2vwaA00	1.20.58.1330	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Plasmodium falciparum UIS3 membrane protein	0.72	55.0	5.14e-01	82.3%	74.7%
2xzmV01	1.10.60.20	Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17	0.69	50.0	5.53e-01	92.4%	100.0%
2dofA00	1.10.10.440	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain	0.69	51.0	5.02e-01	79.7%	74.1%
6lcuA02	1.10.10.470	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Maltooligosyl trehalose synthase; domain 4	0.65	57.0	5.18e-01	97.5%	73.3%
5fszA00	3.40.220.10	Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1	0.63	44.0	3.13e-01	78.5%	23.7%
1u8bA02	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.62	44.0	4.92e-01	100.0%	96.7%
3fbzA01	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.61	50.0	4.72e-01	94.9%	82.4%
2og9A01	3.30.390.10	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain	0.61	53.0	4.56e-01	98.7%	77.7%
1lk3A00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.61	49.0	4.19e-01	91.1%	96.3%
3ff5A00	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	0.61	40.0	4.65e-01	96.2%	100.0%
3oymA01	1.10.340.70	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 ›	0.60	46.0	4.39e-01	82.3%	86.0%
3bf7A00	3.40.50.1820	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain	0.60	51.0	3.60e-01	96.2%	59.2%
1xl3C00	1.20.1280.80	Mainly Alpha › Up-down Bundle › Monooxygenase ›	0.57	41.0	3.95e-01	75.9%	65.9%
7ccmB01	1.10.437.10	Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like	0.56	46.0	3.95e-01	96.2%	72.7%
3nhiA01	1.10.238.20	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain	0.55	40.0	3.28e-01	75.9%	46.3%
1li5A02	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	0.55	39.0	3.88e-01	75.9%	74.7%
4ijaA01	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	0.55	41.0	4.47e-01	97.5%	100.0%
3qbrX00	1.10.437.10	Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like	0.55	44.0	3.65e-01	93.7%	65.8%
1t0fA02	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	0.55	44.0	4.12e-01	89.9%	83.8%
1yz6A02	1.10.150.190	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2	0.54	41.0	4.01e-01	98.7%	74.7%
1d5rA01	3.90.190.10	Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily	0.54	47.0	3.70e-01	100.0%	66.7%
5m38C00	3.30.1330.60	Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain	0.54	42.0	3.80e-01	96.2%	60.5%
4hpqD00	1.10.10.2570	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A ›	0.54	42.0	4.41e-01	100.0%	98.6%
1eblA02	3.40.47.10	Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase	0.53	41.0	3.41e-01	84.8%	60.5%
1x4pA00	1.10.10.790	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module	0.53	37.0	3.98e-01	79.7%	89.4%
1ekjA00	3.40.1050.10	Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase	0.53	38.0	2.82e-01	74.7%	51.0%
3nuwA02	3.30.420.310	Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, C-terminal domain	0.52	44.0	3.30e-01	94.9%	48.8%
1gu9C00	1.20.1290.10	Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like	0.52	43.0	3.50e-01	96.2%	89.3%
2rasA01	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.52	45.0	3.46e-01	100.0%	61.8%
7qovB01	1.10.472.20	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Nitrile hydratase, beta subunit	0.51	37.0	3.33e-01	83.5%	55.6%
1zowA02	3.40.47.10	Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase	0.51	41.0	3.50e-01	92.4%	62.6%
1vw4T01	6.10.330.20	Special › Helix non-globular › Monooxygenase ›	0.50	37.0	3.29e-01	77.2%	56.2%
3ph0C00	1.25.40.1040	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.50	31.0	3.63e-01	98.7%	94.3%

ECOD (41)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3690869	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.77	63.0	5.89e-01	100.0%	72.6%
4952808	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.75	49.0	5.71e-01	74.7%	96.4%
5021354	101.1.2.619 ↗	alpha arrays › HTH › HTH › winged helix domain › HTH_33	0.73	48.0	5.19e-01	74.7%	81.5%
3174238	101.1.1.247 ↗	alpha arrays › HTH › HTH › Three-helical HTH › zf-H2C2	0.72	47.0	4.92e-01	79.7%	74.3%
5008720	101.1.1.548 ↗	alpha arrays › HTH › HTH › Three-helical HTH › HTH_32	0.72	50.0	5.44e-01	78.5%	87.7%
4562321	101.1.1.76 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2	0.72	47.0	5.25e-01	78.5%	88.3%
5003693	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.72	50.0	5.47e-01	79.7%	89.2%
5007660	101.1.1.187 ↗	alpha arrays › HTH › HTH › Three-helical HTH › HTH_33	0.71	50.0	5.42e-01	79.7%	89.2%
4966213	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.71	49.0	5.32e-01	78.5%	87.7%
3952621	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.69	53.0	5.66e-01	100.0%	94.2%
5084007	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.69	51.0	5.21e-01	81.0%	82.7%
3899987	101.1.1.12 ↗	alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_Tc3_2	0.69	47.0	4.61e-01	78.5%	65.9%
5071173	247.1.1.1 ↗	a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B	0.67	60.0	4.02e-01	100.0%	92.9%
3797638	3456.1.1.0 ↗	extended segments › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A	0.65	32.0	2.84e-01	73.4%	32.2%
4943037	101.1.17.1 ↗	alpha arrays › HTH › HTH › FF domain › Ribosomal_S17e	0.64	51.0	5.21e-01	93.7%	89.3%
5057920	101.1.2.54 ↗	alpha arrays › HTH › HTH › winged helix domain › Penicillinase_R	0.63	49.0	4.82e-01	84.8%	94.1%
3959510	2008.1.1.0 ↗	a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like	0.63	45.0	2.85e-01	77.2%	13.7%
4246457	3455.1.1.0 ↗	alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors	0.63	44.0	4.77e-01	78.5%	89.2%
3836454	101.1.1.3 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding	0.63	43.0	4.72e-01	86.1%	95.0%
4380725	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.62	53.0	5.43e-01	97.5%	97.3%
3877773	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.60	38.0	4.10e-01	81.0%	76.9%
4094836	310.2.1.1 ↗	a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF	0.59	43.0	3.35e-01	77.2%	93.3%
4510292	3455.1.1.0 ↗	alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors	0.59	43.0	4.45e-01	89.9%	82.7%
3520226	101.1.1.388 ↗	alpha arrays › HTH › HTH › Three-helical HTH › FLYWCH	0.58	51.0	4.35e-01	98.7%	97.7%
4205790	101.1.1.42 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2	0.57	35.0	3.58e-01	74.7%	61.3%
3471979	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.57	45.0	2.96e-01	87.3%	31.7%
3288678	4033.1.1.1 ↗	alpha arrays › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA_dh_N	0.57	45.0	4.17e-01	86.1%	72.0%
3958293	4033.1.1.0 ↗	alpha arrays › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like	0.56	43.0	3.71e-01	84.8%	52.2%
3510805	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.56	38.0	3.21e-01	96.2%	38.6%
5068269	101.1.2.141 ↗	alpha arrays › HTH › HTH › winged helix domain › HTH_24	0.56	40.0	4.14e-01	75.9%	84.0%
3868871	213.1.1.1 ↗	a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1	0.55	43.0	3.22e-01	84.8%	75.6%
4206301	3455.1.1.0 ↗	alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors	0.55	42.0	4.56e-01	97.5%	100.0%
3515964	101.1.1.76 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2	0.55	46.0	4.32e-01	92.4%	89.7%
3481299	1134.1.1.0 ↗	alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain	0.55	40.0	4.37e-01	98.7%	92.3%
4441325	3455.1.1.0 ↗	alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors	0.54	43.0	4.38e-01	98.7%	87.5%
5012343	101.1.2.554 ↗	alpha arrays › HTH › HTH › winged helix domain › PF30184	0.54	48.0	4.60e-01	98.7%	86.7%
3709217	574.1.1.1 ↗	alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp	0.52	41.0	4.27e-01	92.4%	100.0%
3368995	109.4.1.1525 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase	0.51	41.0	2.87e-01	91.1%	32.1%
3309758	109.4.1.1133 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › C23H4_16c_N	0.51	35.0	2.97e-01	75.9%	39.3%
3261121	3621.1.1.0 ↗	alpha arrays › Dipeptidyl-peptidase 2 helical domain › Dipeptidyl-peptidase 2 helical domain › Dipeptidyl-peptidase 2 helical domain	0.50	34.0	3.15e-01	72.2%	100.0%
3897399	650.1.1.1 ↗	alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ	0.50	36.0	3.59e-01	94.9%	75.0%

D2 medium residues 20-74

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_010087744__Euonymus_yellow_mottle_associated_virus__2586645__D1-67

D3 medium residues 75-192_208-282

PDB

Domain cluster: rep: uncovered_polypeptide_polyprotein__YP_001086452_0-758__Chrysanthemum_virus_B__12165__D72-292

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01660.23 best	Vmethyltransf	133.5	1.30e-38	98.5%	67.5%

D4 medium residues 563-611_787-822

PDB

Domain cluster: representative

D5 medium residues 612-786

PDB

Domain cluster: rep: p39__YP_004928123__Hibiscus_green_spot_virus_2__1513278__D5-179

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01443.25 best	Viral_helicase1	100.1	2.50e-28	68.6%	49.1%

D6 medium residues 823-923

PDB

Domain cluster: rep: TGB1_protein__NP_619560__Garlic_latent_virus__12458__D129-228

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01443.25 best	Viral_helicase1	55.0	1.50e-14	76.2%	31.6%

D7 medium residues 968-1016_1095-1147

PDB

Domain cluster: rep: RdRp__YP_006908997__Diuris_virus_A__1247115__D19-40_76-171

D8 medium residues 1017-1094_1185-1232

PDB

Domain cluster: representative

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2xokP00	1.20.20.10	Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C	0.68	24.0	3.14e-01	88.9%	54.1%
2x2vA00	1.20.20.10	Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C	0.62	24.0	3.26e-01	91.3%	64.7%
2uuiA00	1.20.120.550	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Membrane associated eicosanoid/glutathione metabolism-like domain	0.59	32.0	2.96e-01	97.6%	41.3%
4nooB00	1.10.8.1160	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.54	29.0	3.30e-01	93.7%	69.5%
1ij5A01	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.52	20.0	2.42e-01	87.3%	47.4%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3757568	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.50	22.0	2.40e-01	88.9%	44.8%

D9 medium residues 1148-1184_1233-1301

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181