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RdRp

Euk-Vir

Hubei_permutotetra-like_virus_4

RdRp__YP_009337378__Hubei_permutotetra-like_virus_4__1923078

Identity

Accession:: YP_009337378 ↗
Protein ID:: RdRp
Kingdom:: euk

Quality

67.9 mean pLDDT

Cluster

View cluster (20 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 740-820

PDB

D2 medium residues 1-51_655-695

PDB

D3 medium residues 52-200_273-293_430-451

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	30.5	2.30e-07	24.0%	10.6%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1699894	304.48.2.2 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Permu_RdRp_palm	0.86	83.0	5.80e-01	100.0%	75.0%
None	—		0.76	68.0	4.91e-01	94.3%	88.8%
1145898	304.48.2.1 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Birna_RdRp_palm	0.76	69.0	4.93e-01	95.8%	87.5%

D4 medium residues 201-272_294-334_385-429

PDB

Domain cluster: rep: replicase__YP_009179352__Aphis_glycines_virus_2_Viruses.__X__D99-112_203-276_293-321_386-433

Pfam (3)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	90.5	1.40e-25	46.8%	19.9%
PF22152.2	Permu_RdRp_palm	33.2	3.60e-08	29.1%	12.9%
PF22152.2	Permu_RdRp_palm	41.5	1.10e-10	27.9%	11.5%

D5 medium residues 335-384_452-525

PDB

Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D328-384_485-539

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	76.9	1.90e-21	58.1%	21.0%
PF22152.2	Permu_RdRp_palm	42.9	4.20e-11	41.1%	14.3%

CATH (17)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3ovcA01	3.30.200.150	Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 ›	0.67	32.0	4.16e-01	86.3%	80.3%
1pcfA00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.62	30.0	3.86e-01	83.9%	83.3%
2rqxA00	2.40.50.650	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) ›	0.61	38.0	4.45e-01	85.5%	93.8%
3eb8B01	3.10.450.460	Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › EspG protein, N-terminal domain	0.59	29.0	3.99e-01	82.3%	95.1%
2nvnA00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.58	35.0	3.60e-01	99.2%	60.8%
2it9A00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.58	36.0	3.71e-01	99.2%	64.2%
3a2eA00	3.30.430.20	Alpha Beta › 2-Layer Sandwich › Killer Toxin P4; Chain A › Gnk2 domain, C-X8-C-X2-C motif	0.56	40.0	4.21e-01	81.5%	84.3%
3i7fA01	2.40.50.140	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins	0.56	34.0	3.44e-01	81.5%	58.6%
7uinD01	3.30.70.270	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain	0.55	50.0	4.53e-01	99.2%	85.6%
2e4qA00	2.102.10.10	Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain	0.55	42.0	4.50e-01	96.0%	93.5%
1y8cA02	2.20.25.110	Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases	0.54	28.0	3.74e-01	82.3%	100.0%
4dkaC00	2.40.50.140	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins	0.54	31.0	3.70e-01	80.6%	82.6%
3gceA00	2.102.10.10	Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain	0.53	41.0	4.38e-01	94.4%	97.1%
4aghA00	2.30.31.10	Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A	0.53	30.0	3.58e-01	90.3%	83.7%
4nkbA01	3.30.1120.120	Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain ›	0.52	40.0	4.19e-01	96.0%	87.7%
4u6bA00	2.115.10.20	Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43	0.52	36.0	2.66e-01	71.0%	41.1%
1dmlA00	3.70.10.10	Alpha Beta › Box › Proliferating Cell Nuclear Antigen ›	0.51	37.0	2.93e-01	74.2%	89.9%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1699894	304.48.2.2 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Permu_RdRp_palm	0.92	89.0	5.59e-01	100.0%	37.4%
1140832	809.2.1.1 ↗	a+b two layers › BLIP-like › BT0923-like › BT0923-like › PepSY_like	0.66	25.0	3.43e-01	70.2%	66.7%
4943690	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.62	43.0	4.07e-01	71.0%	70.3%
5035423	295.1.1.0 ↗	a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain	0.60	38.0	4.49e-01	99.2%	94.1%
3700773	7520.1.1.0 ↗	a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like	0.57	45.0	3.99e-01	84.7%	65.6%
5072327	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.56	39.0	3.79e-01	71.0%	67.4%
3308699	3887.2.1.1 ↗	a+b two layers › Yeast killer toxin-like › Antifungal protein ginkbilobin-2 › Antifungal protein ginkbilobin-2 › Stress-antifung	0.56	39.0	4.11e-01	80.6%	80.9%
3313558	3887.2.1.1 ↗	a+b two layers › Yeast killer toxin-like › Antifungal protein ginkbilobin-2 › Antifungal protein ginkbilobin-2 › Stress-antifung	0.55	39.0	4.16e-01	81.5%	83.6%
4947696	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.52	36.0	3.60e-01	72.6%	68.5%
3725227	519.1.1.1 ↗	a+b two layers › mRNA decapping enzyme DcpS N-terminal domain › mRNA decapping enzyme DcpS N-terminal domain › mRNA decapping enzyme DcpS N-terminal domain › DcpS	0.51	29.0	3.48e-01	81.5%	86.3%
3302412	223.1.1.0 ↗	a+b three layers › Profilin-like › sensor domains › sensor domains	0.50	44.0	3.41e-01	100.0%	83.3%

D6 medium residues 526-654

PDB

Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D29-60_540-665

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22260.2 best	Permu_RdRp_thumb	126.1	7.80e-37	77.5%	99.0%

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2pusA04	6.10.140.300	Special › Helix non-globular › Helix Hairpins ›	0.73	57.0	6.22e-01	82.2%	100.0%
1khvA05	1.20.960.20	Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A ›	0.62	43.0	4.83e-01	89.1%	94.8%
3oyxA02	1.20.58.1560	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.54	28.0	3.59e-01	79.1%	92.5%
3vw5A00	1.50.10.10	Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase ›	0.52	46.0	3.26e-01	97.7%	38.3%

ECOD (6)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1712471	4967.1.1.17 ↗	alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Permu_RdRp_thumb	0.92	82.0	7.89e-01	91.5%	85.8%
3671772	109.4.1.420 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR	0.58	39.0	3.56e-01	95.3%	51.8%
3598761	1106.1.1.0 ↗	alpha arrays › RDS3 complex subunit 10 › RDS3 complex subunit 10 › RDS3 complex subunit 10	0.56	22.0	2.69e-01	76.7%	51.9%
3839049	616.1.1.1 ↗	alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15	0.54	37.0	4.37e-01	84.5%	100.0%
4024825	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.53	45.0	3.99e-01	89.9%	77.1%
3714425	109.4.1.210 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19	0.50	35.0	3.74e-01	96.9%	82.6%

D7 medium residues 867-947

PDB