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RdRp

Euk-Vir

Hubei_permutotetra-like_virus_6

RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080

Identity

Accession:: YP_009337318 ↗
Protein ID:: RdRp
Kingdom:: euk

Quality

71.3 mean pLDDT

Cluster

View cluster (20 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 29-60_540-665

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22260.2 best	Permu_RdRp_thumb	99.7	1.30e-28	62.7%	100.0%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1eteA00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.61	35.0	3.76e-01	70.3%	64.9%
2dzlA00	1.10.8.10	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain	0.54	23.0	3.25e-01	92.4%	86.4%

ECOD (3)

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	66.0	7.04e-01	73.4%	83.7%
1578946	4967.1.1.15 ↗	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 › Birna_VP1_thumb	0.66	52.0	5.07e-01	82.3%	82.1%
3829196	109.4.1.1308 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, TPR_24	0.56	31.0	2.55e-01	74.7%	27.8%

D2 high residues 762-850

PDB

D3 high residues 855-957

PDB

D4 medium residues 61-209_279-301

PDB

Domain cluster: rep: non-structural_protein__YP_003038595__Drosophila_A_virus__595895__D1-30_93-129_206-309

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	27.7	1.70e-06	22.1%	6.7%

D5 medium residues 210-278_302-327_385-484

PDB

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

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	115.9	2.60e-33	52.3%	26.3%
PF22152.2	Permu_RdRp_palm	57.6	1.40e-15	35.4%	17.6%

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1r1uB00	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.56	22.0	3.10e-01	73.8%	72.0%
5jbrA01	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.56	23.0	3.29e-01	93.8%	80.2%
1tfkB00	1.20.120.650	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Colicin D	0.54	22.0	3.08e-01	78.5%	76.7%
2guzA00	1.10.287.110	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain	0.54	22.0	3.42e-01	74.9%	98.6%
2wy4A00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.53	35.0	4.05e-01	77.9%	92.8%

ECOD (6)

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	0.97	95.0	6.57e-01	100.0%	52.9%
4954701	101.1.2.554 ↗	alpha arrays › HTH › HTH › winged helix domain › PF30184	0.58	25.0	3.28e-01	77.4%	70.5%
4954698	101.1.2.554 ↗	alpha arrays › HTH › HTH › winged helix domain › PF30184	0.56	24.0	3.32e-01	77.4%	77.9%
3997418	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	0.56	50.0	4.22e-01	98.5%	77.9%
1296342	101.1.2.456 ↗	alpha arrays › HTH › HTH › winged helix domain › HTH_MmpR5	0.54	24.0	2.77e-01	93.8%	51.0%
4937136	101.1.2.650 ↗	alpha arrays › HTH › HTH › winged helix domain › DUF7343	0.51	22.0	2.97e-01	79.0%	76.0%

D6 medium residues 328-384_485-539

PDB

Domain cluster: representative

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22152.2 best	Permu_RdRp_palm	40.9	1.70e-10	57.1%	17.4%
PF22152.2	Permu_RdRp_palm	32.4	6.20e-08	42.9%	12.9%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4pg4B03	3.30.70.3100	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.54	30.0	3.57e-01	75.9%	80.0%
3girA02	3.30.70.1400	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Aminomethyltransferase beta-barrel domains	0.52	31.0	3.43e-01	84.8%	75.6%
7fjlA01	2.102.10.10	Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain	0.52	38.0	3.53e-01	75.9%	80.3%
3ddmA01	3.30.390.10	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain	0.52	35.0	3.44e-01	70.5%	93.6%
7szeB01	2.102.10.10	Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain	0.51	36.0	3.74e-01	74.1%	100.0%
1h8mA00	3.30.450.50	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain	0.50	39.0	3.69e-01	83.9%	72.9%
3f1sA02	2.30.39.10	Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1	0.50	38.0	3.47e-01	80.4%	100.0%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4487967	66.1.1.1 ↗	beta sandwiches › ISP domain › ISP domain › ISP domain › Rieske	0.52	37.0	3.93e-01	74.1%	97.0%
4964362	6030.1.1.1 ↗	a+b two layers › Middle domain of ribosomal protein S2-related protein › Middle domain of ribosomal protein S2-related protein › Middle domain of ribosomal protein S2-related protein › DR2241	0.52	41.0	4.05e-01	84.8%	95.8%
3621288	11.1.4.16 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › EMC7_beta-sandw	0.51	37.0	3.40e-01	92.0%	55.5%
4031542	66.1.1.2 ↗	beta sandwiches › ISP domain › ISP domain › ISP domain › Rieske_2	0.51	36.0	3.85e-01	75.0%	99.0%

D7 medium residues 1014-1065

PDB