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RNA-dependent_RNA_polymerase

Euk-Vir

Xanthophyllomyces_dendrorhous_virus_L1B

RNA-dependent_RNA_polymerase__YP_009507835__Xanthophyllomyces_dendrorhous_virus_L1B__1167691

Identity

Accession:: YP_009507835 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

86.5 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 high residues 9-125

PDB

Domain cluster: representative

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2xzlA02	2.40.30.230	Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 ›	0.59	34.0	3.97e-01	88.0%	82.3%
1mbmA01	2.40.10.10	Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases	0.56	30.0	3.51e-01	75.2%	75.0%
5uaoC00	3.50.50.60	Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain	0.52	42.0	2.75e-01	86.3%	57.0%
2aqjA00	3.50.50.60	Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain	0.51	40.0	2.67e-01	86.3%	59.6%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4500949	1.1.5.80 ↗	beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PF26339	0.60	30.0	3.67e-01	77.8%	74.7%

D2 high residues 135-271_599-614

PDB

Domain cluster: representative

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6h9dA00	1.10.530.40	Mainly Alpha › Orthogonal Bundle › Lysozyme ›	0.54	40.0	4.10e-01	76.5%	100.0%
3u5nA02	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.53	39.0	4.39e-01	84.3%	96.7%
1xg2B00	1.20.140.40	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein	0.53	37.0	3.79e-01	72.5%	98.0%
2ehwA00	6.10.140.1220	Special › Helix non-globular › Helix Hairpins ›	0.52	32.0	3.62e-01	87.6%	80.0%
2rldA00	1.20.1440.60	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence	0.51	36.0	4.07e-01	71.2%	97.4%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3231161	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	0.57	47.0	2.96e-01	89.5%	55.7%
3326634	633.4.1.1 ↗	alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI	0.56	39.0	3.72e-01	70.6%	89.7%

D3 medium residues 273-312_372-440_452-537

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009342055__Trichoderma_atroviride_mycovirus__1934322__D310-326_384-417_467-550_629-645

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	84.0	1.60e-23	86.7%	32.9%

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3umgA02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.65	18.0	2.98e-01	91.3%	63.4%
2r7rA05	1.10.357.80	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 ›	0.64	55.0	5.75e-01	89.7%	100.0%
3u61D03	1.20.272.10	Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 ›	0.56	26.0	3.68e-01	83.1%	91.2%
2d2sA02	1.20.58.1220	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, C-terminal helical domain	0.55	22.0	3.06e-01	83.6%	70.3%
7yb9A01	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.53	22.0	2.18e-01	71.3%	32.6%
2f33A01	1.10.238.10	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand	0.51	21.0	3.31e-01	70.8%	100.0%

ECOD (29)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5366	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	0.81	77.0	5.92e-01	100.0%	67.8%
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	76.0	6.06e-01	100.0%	73.1%
223786	304.48.1.16 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4	0.75	70.0	5.83e-01	99.5%	82.7%
3928801	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	69.0	5.64e-01	100.0%	76.3%
3772920	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	69.0	5.90e-01	100.0%	97.7%
3883010	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	57.0	4.84e-01	79.5%	62.3%
3260077	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	68.0	5.31e-01	100.0%	85.4%
3273928	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	68.0	4.76e-01	100.0%	58.4%
3877925	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	68.0	5.33e-01	100.0%	75.1%
3272030	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	67.0	5.27e-01	99.5%	84.3%
3753267	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	68.0	5.13e-01	100.0%	67.6%
3753579	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	68.0	4.84e-01	100.0%	55.0%
3920615	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	67.0	5.02e-01	99.5%	73.2%
3878013	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	67.0	5.21e-01	99.5%	82.5%
3265091	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	67.0	4.72e-01	99.5%	58.6%
3899435	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	67.0	5.03e-01	99.5%	75.5%
3784946	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	67.0	5.14e-01	100.0%	79.0%
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	0.71	66.0	5.19e-01	99.5%	83.8%
4380832	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	66.0	5.18e-01	100.0%	75.7%
3451410	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	66.0	4.91e-01	100.0%	60.2%
3789227	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	0.69	61.0	5.15e-01	92.8%	97.4%
3766919	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	0.69	64.0	4.32e-01	100.0%	47.7%
3382764	626.1.1.0 ↗	alpha complex topology › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain)	0.69	58.0	3.91e-01	89.2%	35.7%
4424453	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	64.0	4.55e-01	100.0%	59.8%
3422064	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	63.0	4.96e-01	100.0%	82.5%
3708776	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	4.89e-01	95.4%	76.6%
1758636	138.1.1.8 ↗	alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › Gp44_C	0.57	26.0	3.67e-01	80.5%	91.0%
2814210	109.4.1.1427 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_6, TPR_8, TPR_19	0.54	23.0	3.58e-01	76.4%	100.0%
4549638	109.4.1.362 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1,TPR_8	0.53	24.0	2.57e-01	70.3%	45.1%

D4 medium residues 313-371

PDB

Domain cluster: representative

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2gmhA01	3.50.50.60	Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain	0.56	45.0	3.01e-01	91.5%	75.9%
3hzrA02	1.10.240.10	Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase	0.56	44.0	3.76e-01	94.9%	81.1%
2pgsA02	1.10.3550.10	Mainly Alpha › Orthogonal Bundle › eoxyguanosinetriphosphate triphosphohydrolase fold › eoxyguanosinetriphosphate triphosphohydrolase domain-like	0.55	42.0	3.53e-01	91.5%	95.0%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2979132	2007.6.1.1 ↗	a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › Ribosomal_S2	0.50	37.0	2.65e-01	86.4%	86.0%
4393203	140.1.1.4 ↗	alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › tRNA-synt_1e,DALR_2	0.50	36.0	2.61e-01	81.4%	99.5%

D5 medium residues 441-451_538-598

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009342428__Wuhan_insect_virus_26__1923730__D436-447_537-592

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	32.9	5.10e-08	91.7%	11.6%

D6 medium residues 615-667

PDB

Domain cluster: representative

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6m36O01	3.30.565.10	Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain	0.65	53.0	4.52e-01	96.2%	75.0%
2fltA00	3.30.429.10	Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor	0.63	53.0	4.15e-01	96.2%	70.9%
3bs3A00	1.10.260.40	Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains	0.54	40.0	3.89e-01	98.1%	71.7%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4385837	1037.1.1.1 ↗	alpha bundles › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › LGT	0.77	60.0	3.77e-01	86.8%	23.8%
3253487	616.1.1.0 ↗	alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain	0.76	60.0	5.83e-01	88.7%	81.7%
4646369	1037.1.1.1 ↗	alpha bundles › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › LGT	0.73	58.0	3.70e-01	88.7%	27.0%
4964648	2008.1.1.59 ↗	a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1	0.72	60.0	3.94e-01	96.2%	22.1%

D7 medium residues 668-819

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
2m3aA00	1.10.10.1900	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Knl-2 Myb-like DNA-binding domain-like	0.51	21.0	2.95e-01	88.8%	80.6%