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RdRp

Euk-Vir

Aedes_camptorhynchus_negev-like_virus_Viruses.

RdRp__YP_009388601__Aedes_camptorhynchus_negev-like_virus_Viruses.__X

Identity

Accession:: YP_009388601 ↗
Protein ID:: RdRp
Kingdom:: euk

Quality

92.5 mean pLDDT

Cluster

View cluster (85 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 397-476

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	32.9	4.70e-08	97.5%	17.9%

CATH (30)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1dxrL02	1.20.85.10	Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like	0.65	47.0	4.31e-01	77.5%	69.4%
4dmvA01	1.20.58.1190	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.65	48.0	4.79e-01	95.0%	76.5%
1n95A00	1.25.40.120	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Protein prenylyltransferase	0.59	41.0	2.80e-01	97.5%	18.6%
1kz7A01	1.20.900.10	Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain	0.59	50.0	3.81e-01	95.0%	49.7%
3oxfA05	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.59	41.0	4.29e-01	95.0%	78.7%
1vw4L02	1.10.246.170	Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 ›	0.58	47.0	4.68e-01	91.3%	89.4%
2dznF00	1.10.8.60	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.57	30.0	3.24e-01	78.8%	58.0%
4h9nC00	1.20.58.2170	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.57	39.0	2.99e-01	71.2%	40.0%
3cx5A02	3.30.830.10	Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like	0.57	48.0	3.57e-01	96.2%	65.9%
3tl4X02	1.10.10.2420	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A ›	0.57	38.0	3.96e-01	97.5%	76.4%
1yxrA01	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.56	44.0	4.56e-01	93.8%	94.6%
2gs4A00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.56	41.0	3.37e-01	80.0%	84.2%
3axjB02	1.20.58.200	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2	0.55	49.0	4.80e-01	100.0%	98.8%
3a8pA02	6.10.140.680	Special › Helix non-globular › Helix Hairpins ›	0.55	40.0	3.60e-01	77.5%	90.4%
2g38B00	1.20.1260.20	Mainly Alpha › Up-down Bundle › Ferritin › PPE superfamily	0.55	42.0	3.34e-01	83.7%	86.7%
1ds8M02	1.20.85.10	Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like	0.55	40.0	3.25e-01	77.5%	48.1%
6ygiB01	1.10.4090.10	Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus	0.55	39.0	3.27e-01	76.2%	41.8%
5ubvA02	1.10.8.60	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.55	29.0	3.10e-01	80.0%	56.3%
2gscC00	1.20.1440.60	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence	0.55	44.0	4.07e-01	92.5%	67.3%
2dodA00	1.10.10.440	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain	0.54	36.0	3.64e-01	92.5%	67.1%
1xo0A01	1.10.150.130	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain	0.54	40.0	3.62e-01	100.0%	57.7%
1br0A00	1.20.58.70	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.53	44.0	3.98e-01	96.2%	85.8%
3zvkA00	3.40.50.1010	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease	0.53	39.0	3.35e-01	87.5%	47.0%
1rfyB00	1.10.287.160	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat	0.52	39.0	3.85e-01	81.2%	85.2%
3jsbA01	1.20.1440.300	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain	0.52	37.0	3.78e-01	93.8%	74.1%
8ab6B02	3.30.830.10	Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like	0.52	44.0	3.48e-01	98.8%	76.2%
3uitA02	1.20.1270.460	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ›	0.52	43.0	3.79e-01	96.2%	68.5%
5dvwA00	1.20.120.1160	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.52	45.0	3.84e-01	98.8%	59.1%
2ds2D01	1.10.110.10	Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins	0.51	35.0	3.87e-01	80.0%	100.0%
3emlA01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.51	43.0	3.03e-01	97.5%	57.6%

ECOD (33)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3598942	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.65	45.0	4.12e-01	100.0%	55.2%
5041952	603.1.1.0 ↗	alpha bundles › STAT-like › t-snare proteins › t-snare proteins	0.62	52.0	4.43e-01	93.8%	89.6%
3857096	109.4.1.97 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2,TPR_12	0.61	41.0	2.91e-01	93.8%	22.4%
3801688	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.60	51.0	4.72e-01	96.2%	84.8%
3755341	133.1.1.1 ↗	alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF	0.59	50.0	3.75e-01	95.0%	48.1%
3756535	604.1.1.5 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_3	0.59	50.0	4.45e-01	95.0%	77.4%
3898383	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.58	49.0	4.28e-01	95.0%	76.0%
3926031	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.58	48.0	4.59e-01	95.0%	77.9%
5023517	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.58	41.0	3.96e-01	75.0%	85.3%
3755128	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.58	50.0	4.75e-01	96.2%	86.3%
3655114	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.57	45.0	3.75e-01	93.8%	48.6%
3257772	309.1.1.4 ↗	a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C	0.57	48.0	3.57e-01	96.2%	65.5%
3566007	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.57	50.0	4.47e-01	100.0%	83.5%
3855973	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.56	47.0	4.43e-01	95.0%	87.0%
3585163	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.56	47.0	4.35e-01	93.8%	80.0%
3238459	616.1.1.0 ↗	alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain	0.56	32.0	3.50e-01	86.3%	67.7%
4660104	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.56	38.0	4.16e-01	97.5%	86.2%
3398024	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.56	47.0	4.51e-01	95.0%	84.2%
3525705	109.4.1.1653 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Iml2-TPR_39, TPR_8	0.55	47.0	3.11e-01	97.5%	42.7%
3343513	192.8.1.268 ↗	alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › CemA	0.55	41.0	3.81e-01	81.2%	79.8%
3477179	198.1.1.0 ↗	alpha arrays › Saposin-like › Saposin-like › Saposin-like	0.54	40.0	3.94e-01	80.0%	90.6%
3197663	309.1.1.4 ↗	a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C	0.54	45.0	3.49e-01	97.5%	71.2%
3830008	633.4.1.1 ↗	alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI	0.54	43.0	3.59e-01	93.8%	47.7%
3834457	7026.1.1.0 ↗	beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13	0.54	35.0	3.61e-01	73.8%	70.7%
3783873	601.19.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein	0.54	40.0	3.39e-01	80.0%	86.7%
3714155	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.53	45.0	4.29e-01	95.0%	83.2%
3580104	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.53	44.0	4.28e-01	98.8%	89.5%
5016525	103.1.1.0 ↗	alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain	0.53	39.0	4.00e-01	86.3%	78.8%
4530108	3711.1.1.59 ↗	alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › CemA	0.53	40.0	3.83e-01	86.3%	82.8%
3705369	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.52	42.0	3.96e-01	91.3%	77.0%
4998188	1075.1.1.3 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane_2	0.52	45.0	3.26e-01	97.5%	40.0%
5079636	109.1.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C	0.52	39.0	3.75e-01	90.0%	70.5%
3801658	601.4.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains	0.50	42.0	3.64e-01	97.5%	68.9%

D2 medium residues 42-85_280-304

PDB

Domain cluster: representative

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3lxuX01	3.40.50.200	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain	0.55	39.0	2.51e-01	75.4%	36.0%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4980789	304.28.1.0 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain	0.52	38.0	2.40e-01	81.2%	49.9%

D3 medium residues 86-108_120-151_186-211_254-279

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2f76X00	1.10.150.490	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Retroviral GAG p10 protein	0.53	28.0	2.94e-01	78.5%	52.0%
3h36A00	1.10.10.400	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain	0.51	31.0	3.54e-01	77.6%	83.3%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4633929	101.11.1.1 ↗	alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase	0.53	32.0	3.40e-01	74.8%	68.9%

D4 medium residues 212-253_305-396

PDB

Domain cluster: rep: RdRp,_partial__YP_008858531__Carnation_yellow_fleck_virus__940280__D190-234_286-374

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	81.8	6.80e-23	69.4%	19.3%