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RNA-dependent_RNA_polymerase

Euk-Vir

Cronartium_ribicola_mitovirus_3

RNA-dependent_RNA_polymerase__YP_009259482__Cronartium_ribicola_mitovirus_3__1816486

Identity

Accession:: YP_009259482 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

68.5 mean pLDDT

Taxonomy

Orthornavirae› Lenarviricota› Howeltoviricetes› Cryppavirales› Mitoviridae› Unuamitovirus› Cronartium_ribicola_mitovirus_3

TaxID: 1816486

Cluster

View cluster (26 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 high residues 3-116

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009465715__Erysiphe_necator_mitovirus_1__2052561__D5-113

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3sp1A02	1.20.120.1910	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cysteine-tRNA ligase, C-terminal anti-codon recognition domain	0.65	37.0	3.38e-01	90.4%	41.1%
1abvA00	1.10.520.20	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase	0.61	43.0	4.52e-01	99.1%	80.0%
3sqnA02	1.10.1790.40	Mainly Alpha › Orthogonal Bundle › PTS-regulatory domain, PRD ›	0.61	41.0	4.13e-01	96.5%	66.9%
4pxoA02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.56	37.0	3.51e-01	71.9%	57.3%
2wssW01	1.10.520.20	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase	0.55	42.0	4.49e-01	78.9%	100.0%
2c9oB03	1.10.8.60	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.55	31.0	3.65e-01	74.6%	77.1%
1ny9A00	1.10.490.50	Mainly Alpha › Orthogonal Bundle › Globin-like › Antibiotic binding domain of TipA-like multidrug resistance regulators	0.55	37.0	4.05e-01	87.7%	85.1%
4houB00	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.54	36.0	2.80e-01	93.0%	31.4%
2zihC00	1.10.3630.10	Mainly Alpha › Orthogonal Bundle › yeast vps74-n-term truncation variant fold › yeast vps74-n-term truncation variant domain like	0.53	45.0	3.48e-01	95.6%	92.1%
5vjhB02	1.10.8.60	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.53	33.0	3.67e-01	90.4%	78.3%
2xq0A03	1.10.390.10	Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2	0.51	41.0	3.65e-01	85.1%	98.1%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4854884	4963.1.2.1 ↗	alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal domain in vesicular stomatitis virus RNA polymerase L › Mononeg_RNA_pol	0.70	63.0	5.50e-01	100.0%	78.0%
4120183	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	0.68	54.0	4.01e-01	99.1%	32.9%
5025274	1075.1.1.3 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane_2	0.61	47.0	3.62e-01	83.3%	77.8%
4396592	7064.1.1.3 ↗	alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › FUSC_2	0.61	54.0	5.00e-01	100.0%	94.0%
3743981	5081.1.1.2 ↗	alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › DER1	0.56	46.0	3.90e-01	89.5%	87.9%
3640046	4120.1.1.0 ↗	few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP	0.54	48.0	4.23e-01	100.0%	72.0%
3208435	192.8.1.0 ↗	alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain	0.54	48.0	4.05e-01	100.0%	64.6%
4013411	5081.1.1.0 ↗	alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like	0.52	47.0	3.89e-01	100.0%	100.0%
3679552	149.1.1.1 ↗	alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450	0.51	46.0	3.05e-01	100.0%	31.9%
3940746	5067.1.1.3 ↗	alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Patched	0.51	45.0	3.79e-01	100.0%	62.5%
3579769	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.50	40.0	3.69e-01	84.2%	99.3%
3393532	5054.1.1.2 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans	0.50	35.0	2.68e-01	72.8%	40.4%

D2 medium residues 153-243_260-277

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7dniC02	1.10.533.10	Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas	0.54	33.0	3.49e-01	80.7%	68.1%
1imvA02	3.30.497.10	Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2	0.51	39.0	3.23e-01	80.7%	82.0%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3386663	629.1.1.1 ↗	alpha bundles › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › Nitrate_red_del	0.53	40.0	3.36e-01	80.7%	91.8%
3694638	5059.1.1.10 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Sulf_transp	0.51	38.0	2.90e-01	81.7%	79.5%
4015925	5001.1.1.85 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin	0.50	40.0	2.96e-01	86.2%	79.0%
4990841	2004.1.1.29 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD	0.50	37.0	2.36e-01	78.0%	15.7%

D3 medium residues 244-259_321-363

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05919.17 best	Mitovir_RNA_pol	26.9	3.40e-06	74.6%	8.5%

CATH (12)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2wz1B00	3.30.70.1230	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain	0.59	44.0	3.11e-01	83.1%	41.3%
5hnmC00	3.30.1380.10	Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 ›	0.56	41.0	2.99e-01	79.7%	66.9%
2kgfA00	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.53	36.0	2.84e-01	72.9%	50.0%
3d6wB02	2.20.25.10	Mainly Beta › Single Sheet › N-terminal domain of TfIIb ›	0.52	23.0	2.70e-01	74.6%	43.6%
6ui4A01	1.20.120.720	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain	0.52	35.0	3.19e-01	72.9%	64.8%
1h2iA01	3.30.390.80	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › DNA repair protein Rad52/59/22	0.51	38.0	2.95e-01	83.1%	80.4%
2o5aA01	3.30.460.10	Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2	0.51	38.0	3.23e-01	81.4%	82.4%
4ifeA02	3.30.420.240	Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 ›	0.51	41.0	2.89e-01	96.6%	48.0%
3ke3A02	3.40.640.10	Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain)	0.51	35.0	2.28e-01	72.9%	70.3%
3e8mA00	3.40.50.1000	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like	0.51	41.0	3.07e-01	93.2%	72.0%
2gaxA00	3.40.1490.10	Alpha Beta › 3-Layer(aba) Sandwich › Bit1 › Bit1	0.50	35.0	2.71e-01	72.9%	82.1%
2xfmA00	2.170.260.10	Mainly Beta › Beta Complex › paz domain › paz domain	0.50	35.0	2.82e-01	72.9%	88.3%

ECOD (7)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3577414	2485.1.1.40 ↗	a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › GST_N_3	0.65	45.0	3.35e-01	72.9%	28.7%
3959944	3826.1.1.95 ↗	alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › RNA_pol_Rpb1_1	0.58	42.0	3.64e-01	78.0%	83.2%
3601833	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.56	39.0	2.25e-01	72.9%	15.2%
4987009	3837.1.1.1 ↗	alpha bundles › Uncharacterized conserved protein Dip1984 › Uncharacterized conserved protein Dip1984 › Uncharacterized conserved protein Dip1984 › DUF6847	0.55	37.0	2.86e-01	71.2%	95.3%
3751034	2484.1.1.145 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_7	0.55	39.0	2.59e-01	76.3%	100.0%
3707372	7039.1.1.0 ↗	a+b complex topology › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM	0.53	36.0	2.41e-01	71.2%	31.9%
4970421	304.28.1.0 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain	0.52	42.0	2.96e-01	93.2%	88.1%

D4 medium residues 278-320_364-452

PDB

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

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05919.17 best	Mitovir_RNA_pol	119.5	2.80e-34	67.4%	17.5%
PF05919.17	Mitovir_RNA_pol	47.4	2.10e-12	32.6%	8.6%

D5 medium residues 465-559

PDB