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RNA-dependent_RNA_polymerase

Euk-Vir

Beihai_weivirus-like_virus_7

RNA-dependent_RNA_polymerase__YP_009337047__Beihai_weivirus-like_virus_7__1922754

Identity

Accession:: YP_009337047 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

84.8 mean pLDDT

Cluster

View cluster (18 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 6-140

PDB

Domain cluster: representative

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1u84A00	1.10.340.20	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Apc36109-like domain	0.65	34.0	4.21e-01	73.3%	82.7%
2khvA01	1.10.150.130	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain	0.61	31.0	3.76e-01	71.9%	75.3%
2qsbA00	1.20.1440.50	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like	0.60	34.0	4.16e-01	79.3%	88.2%
2pgeA01	3.30.390.10	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain	0.57	39.0	4.02e-01	83.7%	73.2%
4ex8A00	3.40.1790.10	Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain	0.53	38.0	2.94e-01	74.1%	50.5%
3msyA01	3.30.390.10	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain	0.52	36.0	3.94e-01	84.4%	87.4%
1or4B00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.52	36.0	3.46e-01	71.9%	100.0%

ECOD (5)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3789349	221.1.1.54 ↗	a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Ras_bdg_2	0.57	26.0	2.76e-01	83.7%	44.5%
4954426	1075.5.1.4 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt	0.55	45.0	3.83e-01	85.2%	56.2%
5011383	304.163.1.0 ↗	a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain	0.51	22.0	3.14e-01	83.0%	88.3%
4974991	131.1.1.10 ↗	alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_3	0.51	38.0	3.40e-01	79.3%	88.5%
3284826	5081.1.1.1 ↗	alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid	0.50	40.0	3.49e-01	87.4%	74.1%

D2 high residues 542-600

PDB

Domain cluster: representative

CATH (9)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6b10A00	3.75.10.10	Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A	0.58	50.0	3.17e-01	100.0%	51.4%
4l22A01	3.40.50.2000	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B;	0.57	48.0	2.96e-01	100.0%	56.9%
3m4xA02	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.57	49.0	3.18e-01	100.0%	38.8%
3a27A00	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.57	49.0	3.38e-01	100.0%	38.8%
5zctA01	3.40.50.20	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold ›	0.56	48.0	3.95e-01	100.0%	68.4%
7tjbA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.55	48.0	3.30e-01	100.0%	89.3%
1tkjA00	3.40.630.10	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases	0.53	44.0	2.96e-01	100.0%	48.4%
3dc4A00	3.40.850.10	Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain	0.53	43.0	2.88e-01	100.0%	96.6%
2i7xA02	3.40.50.10890	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold ›	0.51	42.0	3.07e-01	98.3%	57.4%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5046502	2003.1.10.0 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain	0.58	50.0	4.37e-01	98.3%	85.6%
4278951	301.7.1.7 ↗	a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › FIST	0.56	46.0	4.14e-01	93.2%	84.7%
4961619	7577.1.1.2 ↗	a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_3	0.55	43.0	2.63e-01	84.7%	86.7%
3594603	3012.1.1.0 ↗	a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain	0.53	37.0	3.21e-01	74.6%	58.0%
5054979	7533.1.1.1 ↗	a/b three-layered sandwiches › Phosphoglycerate kinase domain 2 › Phosphoglycerate kinase domain 2 › Phosphoglycerate kinase domain 2 › PGK	0.52	43.0	3.06e-01	100.0%	80.0%
259870	2003.1.2.18 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain	0.52	44.0	2.89e-01	96.6%	97.5%
3723619	5051.1.1.10 ↗	alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2	0.51	40.0	2.40e-01	89.8%	99.0%
4962828	283.2.1.20 ↗	a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › DUF7261	0.51	40.0	3.28e-01	93.2%	76.8%
4958637	213.1.1.1 ↗	a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1	0.51	44.0	3.28e-01	100.0%	57.0%
4135068	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.51	38.0	2.38e-01	88.1%	32.3%
4938701	101.1.2.941 ↗	alpha arrays › HTH › HTH › winged helix domain › PF26385	0.50	40.0	3.07e-01	89.8%	77.9%

D3 medium residues 251-280_337-378_476-514

PDB

Domain cluster: representative

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T 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	0.78	54.0	4.04e-01	70.3%	62.8%
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	0.78	54.0	3.94e-01	71.2%	61.4%
None	—		0.76	53.0	3.63e-01	71.2%	48.5%
1697857	304.48.1.30 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › CPV_RdRP_pol_dom	0.71	63.0	4.44e-01	98.2%	84.9%

D4 medium residues 281-336_379-475_515-527

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337141__Beihai_weivirus-like_virus_15__1922743__D392-442_461-485_531-592

D5 medium residues 604-746

PDB

Domain cluster: representative

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3eslA02	1.25.40.930	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.60	39.0	4.18e-01	93.0%	77.3%
2azjA00	1.10.600.10	Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase	0.52	36.0	2.98e-01	71.3%	55.8%
6wy9B01	1.10.540.10	Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain	0.50	28.0	3.08e-01	91.6%	63.8%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3463158	601.18.1.1 ↗	alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 › PsbQ	0.52	38.0	4.10e-01	99.3%	91.6%
4509501	142.1.1.3 ↗	alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2	0.51	28.0	3.10e-01	88.8%	66.4%