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RNA-dependent_RNA_polymerase

Euk-Vir

Wad_Medani_virus

RNA-dependent_RNA_polymerase__YP_009158877__Wad_Medani_virus__40067

Identity

Accession:: YP_009158877 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

86.3 mean pLDDT

Cluster

View cluster (29 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 659-721

PDB

Domain cluster: rep: VP1_protein__YP_009507680__Corriparta_virus__40053__D646-703

D2 medium residues 380-444_500-570_600-654

PDB

Domain cluster: rep: VP1__YP_009507705__Eubenangee_virus__40056__D405-452_477-499_532-575_601-629

Pfam (3)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05788.19 best	Orbi_VP1	84.9	3.70e-24	38.2%	5.6%
PF05788.19	Orbi_VP1	107.2	6.90e-31	37.7%	5.5%
PF05788.19	Orbi_VP1	69.4	1.80e-19	29.3%	4.2%

D3 medium residues 445-499

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05788.19 best	Orbi_VP1	50.5	9.00e-14	100.0%	4.0%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2bs2B01	3.10.20.30	Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain	0.66	45.0	3.61e-01	70.9%	81.1%
3i3lA02	3.30.390.160	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 ›	0.64	39.0	3.05e-01	70.9%	26.4%
1zoyB01	3.10.20.30	Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain	0.64	44.0	3.55e-01	72.7%	79.2%
4cbgD02	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.57	43.0	3.24e-01	90.9%	29.8%
2d42A01	2.170.15.10	Mainly Beta › Beta Complex › Proaerolysin; Chain A, domain 3 › Proaerolysin, chain A, domain 3	0.56	44.0	3.08e-01	87.3%	77.2%
5axmB00	3.30.70.3000	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1)	0.52	44.0	2.93e-01	100.0%	75.3%
1ffyA01	3.40.50.620	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs	0.51	37.0	2.28e-01	83.6%	13.1%

ECOD (9)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4992749	629.1.1.1 ↗	alpha bundles › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › Nitrate_red_del	0.58	47.0	3.14e-01	94.5%	41.6%
3940677	207.1.1.0 ↗	beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats	0.58	46.0	3.19e-01	89.1%	56.4%
4054285	5.1.4.139 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40_2	0.56	43.0	2.54e-01	85.5%	79.2%
4013676	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.55	38.0	2.98e-01	72.7%	67.5%
3276865	2492.1.1.0 ↗	a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like	0.53	40.0	3.38e-01	83.6%	83.0%
3385549	2004.1.1.156 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_5	0.53	43.0	3.07e-01	98.2%	70.8%
3197773	10.12.1.52 ↗	beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_8	0.52	42.0	2.67e-01	92.7%	24.1%
3268123	192.15.1.184 ↗	alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › RA	0.52	37.0	3.01e-01	76.4%	73.3%
3597631	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.51	35.0	2.32e-01	70.9%	32.7%

D4 medium residues 1115-1199

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05788.19 best	Orbi_VP1	104.8	3.70e-30	100.0%	6.5%

CATH (20)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2da3A01	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.67	38.0	4.63e-01	75.3%	100.0%
1o4xA02	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.65	40.0	4.58e-01	70.6%	94.4%
3lcnB00	1.10.340.40	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain	0.64	52.0	4.97e-01	87.1%	79.4%
3g2bA00	1.10.10.1150	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD)	0.64	40.0	4.01e-01	82.4%	60.0%
1rr7A02	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.60	33.0	4.12e-01	75.3%	93.8%
1rr7A01	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.59	30.0	3.78e-01	77.6%	87.0%
4l7aA00	3.40.390.70	Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) ›	0.58	43.0	3.10e-01	80.0%	75.5%
6b8hO01	1.10.520.20	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase	0.58	47.0	4.58e-01	94.1%	99.0%
4jrrB00	3.40.30.10	Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin	0.56	49.0	3.87e-01	100.0%	88.6%
1whuA00	1.10.10.400	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain	0.55	40.0	3.78e-01	76.5%	73.1%
1vdyA00	1.25.40.90	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.55	33.0	2.86e-01	92.9%	35.7%
1b72A00	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.55	37.0	4.04e-01	96.5%	88.2%
3uitA02	1.20.1270.460	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ›	0.55	41.0	3.62e-01	81.2%	86.2%
2remB00	3.40.30.10	Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin	0.54	47.0	3.71e-01	100.0%	86.1%
1bedA00	3.40.30.10	Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin	0.54	47.0	3.75e-01	100.0%	86.7%
3llkA02	1.20.120.310	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain	0.54	39.0	3.35e-01	77.6%	84.6%
2gh1A02	1.10.150.350	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 ›	0.54	47.0	4.30e-01	94.1%	94.4%
2es9A00	1.20.1290.30	Mainly Alpha › Up-down Bundle › AhpD-like ›	0.53	39.0	3.72e-01	77.6%	66.0%
4zbwA02	1.10.533.10	Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas	0.53	40.0	3.98e-01	81.2%	100.0%
3cl3A02	1.10.533.10	Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas	0.52	39.0	3.91e-01	83.5%	100.0%

ECOD (19)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3297949	592.7.1.2 ↗	alpha arrays › PWI domain-like › GIPC1 GH2 domain › GIPC1 GH2 domain › PWI	0.76	55.0	6.13e-01	83.5%	100.0%
3275070	592.1.1.1 ↗	alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI	0.71	49.0	4.97e-01	82.4%	71.8%
5072522	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.69	41.0	4.93e-01	74.1%	92.7%
5030241	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.69	41.0	4.72e-01	76.5%	83.3%
3936170	4964.1.1.0 ↗	alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I	0.64	50.0	4.16e-01	83.5%	67.6%
None	—		0.63	47.0	4.83e-01	84.7%	83.7%
3721641	5067.1.1.8 ↗	alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › HPP	0.62	47.0	3.85e-01	83.5%	86.7%
3230818	101.1.1.1 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain	0.60	38.0	4.04e-01	74.1%	72.0%
3889817	101.1.1.1 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain	0.60	39.0	4.03e-01	71.8%	70.0%
4931472	2.1.1.0 ↗	beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein	0.60	52.0	3.96e-01	96.5%	94.0%
160865	101.1.1.1 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain	0.60	41.0	4.20e-01	76.5%	75.0%
3478184	101.1.1.1 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain	0.59	38.0	3.62e-01	71.8%	54.0%
3168643	592.1.1.2 ↗	alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI	0.58	49.0	4.79e-01	96.5%	88.4%
3760172	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.57	37.0	3.80e-01	75.3%	68.8%
4413254	2485.1.1.10 ↗	a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DSBA	0.56	48.0	3.82e-01	100.0%	87.3%
4061431	190.1.1.0 ↗	alpha arrays › HMG-box-like › HMG-box › HMG-box	0.53	29.0	3.44e-01	84.7%	86.0%
None	—		0.52	41.0	2.78e-01	87.1%	59.2%
4304916	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	0.51	42.0	3.99e-01	91.8%	77.0%
4928781	2004.1.1.156 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_5	0.51	37.0	2.50e-01	78.8%	33.2%