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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_noda-like_virus_8

RNA-dependent_RNA_polymerase__YP_009337881__Hubei_noda-like_virus_8__1922988

Identity

Accession:: YP_009337881 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

71.0 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 185-375

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337879__Hubei_noda-like_virus_9__1922989__D136-259_287-345

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF19222.6 best	Noda_Vmethyltr	169.3	6.40e-50	74.4%	93.2%

D2 high residues 429-521

PDB

Domain cluster: representative

CATH (15)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4huqS00	1.10.1760.20	Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 ›	0.67	49.0	4.02e-01	84.9%	43.3%
2it9A00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.59	53.0	4.88e-01	98.9%	96.7%
2nvnA00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.58	52.0	4.83e-01	100.0%	93.3%
2b8iA00	1.20.1280.100	Mainly Alpha › Up-down Bundle › Monooxygenase › Pas factor, saposin domain	0.58	37.0	4.02e-01	81.7%	77.9%
1df0A02	3.90.70.10	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases	0.58	36.0	3.62e-01	100.0%	62.0%
1u84A00	1.10.340.20	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Apc36109-like domain	0.57	45.0	4.82e-01	96.8%	98.8%
2jpnA00	1.20.1280.210	Mainly Alpha › Up-down Bundle › Monooxygenase › Uncharacterised protein UvsW.1	0.56	33.0	3.55e-01	78.5%	67.1%
2ra1A01	1.20.58.790	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.56	33.0	3.31e-01	93.5%	55.1%
3okqA00	1.20.58.1540	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain	0.54	33.0	3.01e-01	95.7%	44.0%
2hszA02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.54	36.0	3.96e-01	79.6%	86.7%
2rajA02	3.30.1520.10	Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain	0.53	39.0	3.57e-01	78.5%	92.1%
3sqiA01	1.10.150.540	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 ›	0.53	39.0	3.86e-01	90.3%	75.8%
2bjfA01	3.60.60.10	Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A	0.52	40.0	2.81e-01	82.8%	43.4%
1b06A01	1.10.287.990	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain	0.51	32.0	3.57e-01	95.7%	86.6%
1cqxA01	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.51	39.0	3.43e-01	84.9%	57.3%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3224502	101.1.1.75 ↗	alpha arrays › HTH › HTH › Three-helical HTH › HTH_48	0.66	39.0	4.70e-01	81.7%	98.2%
3244407	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.62	37.0	4.39e-01	79.6%	91.7%
4027714	592.2.1.2 ↗	alpha arrays › PWI domain-like › YugE-like › YugE-like › WGG	0.56	46.0	4.43e-01	94.6%	77.3%
3742527	5.1.4.342 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_EDC4L	0.55	42.0	2.76e-01	83.9%	42.2%
3264673	101.1.2.498 ↗	alpha arrays › HTH › HTH › winged helix domain › PF25870	0.55	43.0	3.89e-01	86.0%	78.5%
3478267	3812.1.1.0 ↗	alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE	0.53	31.0	3.38e-01	95.7%	69.3%
3477205	592.2.1.2 ↗	alpha arrays › PWI domain-like › YugE-like › YugE-like › WGG	0.53	45.0	4.34e-01	94.6%	87.6%
3798524	277.1.1.0 ↗	a+b two layers › PX domain › PX domain › PX domain	0.53	42.0	3.89e-01	83.9%	93.0%
3455464	5050.1.1.1 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr	0.51	30.0	2.54e-01	94.6%	33.5%
3980428	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	0.51	29.0	3.13e-01	95.7%	65.3%
3222419	331.23.1.0 ↗	a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain	0.51	34.0	3.64e-01	97.8%	84.0%
4451022	220.1.1.0 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like	0.51	42.0	3.92e-01	100.0%	71.7%

D3 high residues 563-581_895-1035

PDB

Domain cluster: rep: hypothetical_protein__YP_009329984__Beihai_noda-like_virus_29__1922483__D408-447_732-867

D4 medium residues 31-157

PDB

D5 medium residues 582-599_632-711_764-802

PDB

Domain cluster: representative

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2r7rA05	1.10.357.80	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 ›	0.64	57.0	5.27e-01	97.1%	98.9%

ECOD (9)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
217141	304.48.1.15 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3	0.80	75.0	5.40e-01	100.0%	72.3%
4108146	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	0.75	62.0	4.56e-01	86.9%	59.1%
3939319	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	65.0	4.64e-01	95.6%	67.6%
3927049	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	4.75e-01	100.0%	63.4%
4188583	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	4.68e-01	98.5%	57.1%
3918122	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	4.66e-01	98.5%	63.3%
3574984	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	4.73e-01	100.0%	66.9%
3473558	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	58.0	4.90e-01	89.1%	99.6%
4937067	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	4.31e-01	86.9%	65.7%

D6 medium residues 600-631_712-763_844-894

PDB

Domain cluster: representative

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1mukA02	3.90.1850.10	Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3	0.68	62.0	4.18e-01	100.0%	78.8%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4004145	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	0.55	51.0	4.34e-01	100.0%	82.3%
5018488	304.25.1.1 ↗	a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer	0.51	35.0	2.96e-01	70.4%	62.6%