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RNA-dependent_RNA_polymerase

Euk-Vir

Maize-associated_totivirus_3

RNA-dependent_RNA_polymerase__YP_009448194__Maize-associated_totivirus_3__2057198

Identity

Accession:: YP_009448194 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

87.4 mean pLDDT

Cluster

View cluster (56 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 medium residues 1-94

PDB

Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_009182195__Red_clover_powdery_mildew-associated_totivirus_7__1714368__D7-83

D2 medium residues 95-269

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009507835__Xanthophyllomyces_dendrorhous_virus_L1B__1167691__D135-271_599-614

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6h7bA01	1.10.1900.10	Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › c-terminal domain of poly(a) binding protein	0.63	28.0	4.11e-01	76.0%	95.9%
1f1mA00	1.20.120.240	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Lipoprotein, type 6	0.52	29.0	3.10e-01	89.1%	60.5%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3284180	109.3.1.160 ↗	alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › EccD	0.56	30.0	3.24e-01	91.4%	60.0%

D3 medium residues 270-282_314-412_453-515

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	40.2	3.10e-10	62.9%	21.3%

D4 medium residues 283-313_413-452_516-607

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	58.3	1.00e-15	57.1%	18.9%

CATH (17)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5jxsA02	3.30.70.270	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain	0.75	57.0	6.12e-01	78.5%	98.6%
4hkqA01	3.30.70.270	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain	0.74	58.0	6.17e-01	96.9%	92.4%
3mmlF01	3.30.1360.40	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 ›	0.67	31.0	4.31e-01	76.7%	89.9%
1hi8A03	3.30.70.1600	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.65	54.0	5.27e-01	86.5%	92.6%
3va7A05	3.30.1360.40	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 ›	0.62	34.0	4.25e-01	77.9%	86.0%
2zfzD00	3.30.1360.40	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 ›	0.60	27.0	3.81e-01	74.2%	87.3%
2dt9A01	3.30.70.260	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain	0.60	29.0	4.09e-01	77.3%	100.0%
4wp3C00	3.30.70.1230	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain	0.58	43.0	4.14e-01	76.7%	90.9%
1y10B02	3.30.70.1230	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain	0.58	41.0	3.97e-01	72.4%	94.0%
1pqxA00	3.30.1370.70	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Scaffold protein Nfu/NifU, N-terminal domain	0.58	31.0	4.11e-01	76.1%	94.5%
1s5jA03	3.90.1600.10	Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain	0.55	45.0	4.59e-01	85.9%	96.8%
1vk3A01	3.90.650.10	Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain	0.54	40.0	3.80e-01	74.8%	83.4%
2x7iA02	3.30.70.890	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain	0.54	38.0	4.23e-01	90.2%	91.4%
3u0oA02	3.90.650.10	Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain	0.52	39.0	3.80e-01	79.1%	100.0%
5x68A00	3.50.50.60	Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain	0.50	40.0	3.12e-01	82.8%	55.2%
1zj8A02	3.90.480.10	Alpha Beta › Alpha-Beta Complex › Sulfite Reductase Hemoprotein; domain 2 › Sulfite Reductase Hemoprotein;Domain 2	0.50	37.0	3.87e-01	76.7%	84.9%
2oi2A02	3.30.70.890	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain	0.50	37.0	4.04e-01	83.4%	92.5%

ECOD (13)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
None	—		0.74	60.0	4.59e-01	85.9%	100.0%
3937215	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	0.71	60.0	4.46e-01	89.0%	87.1%
5002351	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	0.68	59.0	4.46e-01	93.3%	79.2%
3336938	304.48.1.43 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol	0.67	62.0	5.32e-01	99.4%	94.0%
3068775	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	0.66	54.0	4.99e-01	85.3%	84.2%
3958119	306.6.1.0 ↗	a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like	0.66	31.0	4.12e-01	77.9%	83.5%
4142179	306.2.1.1 ↗	a+b two layers › Glucose permease domain IIB-like › arginine repressor C terminal domain-related › C-terminal domain of arginine repressor › Arg_repressor_C	0.66	30.0	4.33e-01	76.7%	94.7%
4361292	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	0.65	59.0	4.19e-01	96.9%	80.6%
4891214	306.6.1.1 ↗	a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like › CT_C_D	0.65	30.0	3.91e-01	76.7%	75.5%
4035959	306.2.1.1 ↗	a+b two layers › Glucose permease domain IIB-like › arginine repressor C terminal domain-related › C-terminal domain of arginine repressor › Arg_repressor_C	0.64	32.0	4.32e-01	74.8%	91.8%
3495499	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	0.61	55.0	4.42e-01	95.7%	90.2%
4027647	3122.1.1.0 ↗	a+b complex topology › MESD › MESD › MESD	0.61	37.0	4.32e-01	70.6%	85.2%
3987886	306.2.1.1 ↗	a+b two layers › Glucose permease domain IIB-like › arginine repressor C terminal domain-related › C-terminal domain of arginine repressor › Arg_repressor_C	0.56	26.0	3.69e-01	75.5%	93.3%

D5 medium residues 608-686

PDB

Domain cluster: rep: putative_RNA-dependent_RNA_polymerase__YP_009259486__Maize-associated_totivirus_2__1874267__D618-677

D6 medium residues 687-833

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009342428__Wuhan_insect_virus_26__1923730__D637-812

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5l3wA01	1.20.120.140	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain	0.58	28.0	3.66e-01	79.6%	81.0%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3226591	5054.1.1.0 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels	0.63	33.0	3.42e-01	70.7%	52.1%
3760775	103.4.1.2 ↗	alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › TFIIS_M	0.55	33.0	4.05e-01	87.8%	95.6%
3243984	524.1.1.0 ↗	alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p	0.55	34.0	3.73e-01	98.0%	72.8%