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RNA-dependent_RNA_polymerase

Euk-Vir

Changjiang_narna-like_virus_4

RNA-dependent_RNA_polymerase__YP_009337385__Changjiang_narna-like_virus_4__1922779

Identity

Accession:: YP_009337385 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

77.6 mean pLDDT

Cluster

View cluster (11 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 334-486_528-555

PDB

Domain cluster: rep: replication_associated_protein__YP_009345107__Amphibola_crenata_associated_bacilladnavirus_1__1941435__D302-478

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00910.29 best	RNA_helicase	97.4	9.50e-28	58.0%	98.1%

D2 medium residues 8-108

PDB

Domain cluster: representative

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3qwuA01	3.10.450.740	Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, ›	0.56	27.0	3.53e-01	78.2%	93.6%
3g3oA00	3.20.100.30	Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain	0.54	42.0	3.12e-01	85.1%	38.1%
1pj5A03	3.30.1360.120	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1	0.51	44.0	3.65e-01	100.0%	83.3%
7bqiA01	1.20.58.900	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain	0.51	37.0	3.33e-01	78.2%	98.7%
6ruiB04	3.90.1110.10	Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2	0.50	42.0	3.52e-01	94.1%	54.9%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5023940	4312.1.1.0 ↗	a+b two layers › RelE-like › RelE-like › RelE-like	0.59	34.0	4.03e-01	96.0%	82.9%
3687425	7579.1.1.56 ↗	a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_4	0.57	44.0	2.81e-01	84.2%	49.5%
5044803	2498.1.1.6 ↗	mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M3	0.55	46.0	2.91e-01	91.1%	43.1%
4647064	211.1.1.0 ↗	a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	0.55	25.0	3.14e-01	77.2%	70.0%
4978628	2498.1.1.0 ↗	mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain"	0.55	46.0	2.88e-01	93.1%	41.9%
3589150	2498.1.1.7 ↗	mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M3,Peptidase_M3_N	0.55	45.0	2.85e-01	92.1%	41.6%
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	45.0	3.45e-01	97.0%	96.9%
3921414	4357.1.1.1 ↗	beta barrels › WWE domain › WWE domain › WWE domain › WWE	0.53	27.0	2.97e-01	95.0%	59.5%
5069690	243.6.1.0 ↗	a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain	0.53	27.0	3.21e-01	93.1%	73.8%
5033726	101.1.2.55 ↗	alpha arrays › HTH › HTH › winged helix domain › SMC_ScpB	0.51	32.0	3.31e-01	86.1%	65.0%

D3 medium residues 109-233

PDB

Domain cluster: representative

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2k3oA00	1.10.274.60	Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain	0.68	45.0	4.50e-01	100.0%	64.3%
3dl1A01	1.10.472.150	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Glucose-regulated metallo-peptidase M90, N-terminal domain	0.57	34.0	3.73e-01	83.2%	72.7%
2b4vA02	3.30.460.50	Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 ›	0.56	34.0	3.51e-01	100.0%	61.3%
1grlB01	1.10.560.10	Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain	0.53	47.0	3.86e-01	100.0%	92.6%
6ks6a01	1.10.560.10	Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain	0.53	47.0	3.68e-01	100.0%	86.6%
5ulcX00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.51	37.0	3.82e-01	100.0%	79.5%
6gs4A00	1.20.1250.20	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains	0.50	43.0	2.96e-01	95.2%	67.7%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3218028	180.1.1.1 ↗	alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2	0.60	49.0	4.00e-01	87.2%	91.1%
3514804	3722.1.1.0 ↗	alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain	0.58	32.0	2.54e-01	88.8%	27.1%
3630462	192.2.1.2 ↗	alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin	0.58	31.0	2.98e-01	100.0%	45.0%
4797704	5054.1.1.2 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans	0.58	39.0	4.11e-01	100.0%	75.0%
1694871	1015.1.1.0 ↗	alpha complex topology › Insulin-induced gene (Insig) homologs › Insulin-induced gene (Insig) homologs › Insulin-induced gene (Insig) homologs	0.55	49.0	4.29e-01	97.6%	88.9%
3273448	593.1.1.1 ↗	alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like › Cpn60_TCP1	0.54	48.0	3.91e-01	100.0%	93.1%
5000789	192.2.1.1 ↗	alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2	0.53	29.0	3.13e-01	98.4%	61.9%
4410759	192.2.1.2 ↗	alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin	0.53	29.0	3.01e-01	100.0%	54.8%
3397472	192.29.1.203 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › IQUB	0.52	29.0	3.05e-01	86.4%	58.3%
4400946	4018.1.1.2 ↗	a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › Inositol_P	0.52	36.0	3.41e-01	71.2%	72.7%
3394492	180.1.1.1 ↗	alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2	0.51	45.0	3.56e-01	100.0%	78.2%

D4 medium residues 234-324_617-649_692-741

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009333153__Beihai_narna-like_virus_14__1922441__D77-145_426-451_481-543

D5 medium residues 650-691_742-826

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588

D6 medium residues 859-920_933-996

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009336759__Hubei_narna-like_virus_12__1922942__D905-1002_1014-1026

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4c0kA01	1.10.238.10	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand	0.52	30.0	3.32e-01	82.5%	69.3%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3396532	377.1.1.18 ↗	few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-AD	0.55	27.0	3.26e-01	76.2%	70.0%
3719509	524.1.1.1 ↗	alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC	0.53	37.0	3.54e-01	73.0%	70.8%
3988991	181.1.1.1 ↗	alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N	0.51	30.0	3.49e-01	77.8%	81.1%

D7 medium residues 921-932_997-1065

PDB