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RNA-dependent_RNA_polymerase

Euk-Vir

Leptopilina_boulardi_Toti-like_virus

RNA-dependent_RNA_polymerase__YP_009072448__Leptopilina_boulardi_Toti-like_virus__1353795

Identity

Accession:: YP_009072448 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

83.2 mean pLDDT

Taxonomy

Orthornavirae› Duplornaviricota› Chrymotiviricetes› Ghabrivirales› Lebotiviridae› Lebotivirus› Leptopilina_boulardi_Toti-like_virus

TaxID: 1353795

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 4-138

PDB

Domain cluster: representative

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5n13A00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.52	39.0	4.29e-01	83.0%	100.0%
3aqbA00	1.20.120.1450	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.51	33.0	3.32e-01	79.3%	63.0%
2yqdA00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.51	40.0	4.20e-01	82.2%	92.5%
3k2jA00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.51	39.0	4.11e-01	80.7%	90.1%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3814534	633.4.1.1 ↗	alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI	0.51	38.0	3.66e-01	77.0%	96.0%
3181670	109.4.1.356 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans	0.50	33.0	2.26e-01	97.8%	19.1%

D2 medium residues 139-292_333-398

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2r7rA05	1.10.357.80	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 ›	0.70	54.0	6.00e-01	96.4%	100.0%

ECOD (6)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3615272	304.48.1.25 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4	0.64	52.0	4.24e-01	83.6%	60.5%
4071235	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	0.64	49.0	3.73e-01	79.5%	39.6%
3792091	304.48.1.25 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4	0.64	51.0	4.34e-01	82.7%	60.3%
3598902	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	0.64	51.0	4.19e-01	82.7%	60.8%
4516798	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	0.64	50.0	3.89e-01	80.9%	44.6%
3607472	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.51	25.0	2.64e-01	86.4%	47.8%

D3 medium residues 293-332_399-486

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009336893__Sanxia_water_strider_virus_20__1923404__D285-322_387-475

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	32.0	9.60e-08	67.2%	15.9%

D4 medium residues 487-537

PDB

Domain cluster: representative

CATH (9)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2nn4A00	1.10.287.760	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like	0.74	53.0	5.01e-01	88.2%	62.9%
2xseA00	1.20.120.1440	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain	0.68	55.0	3.96e-01	92.2%	55.3%
1dlwA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.66	55.0	4.23e-01	94.1%	80.2%
4v3iA00	1.25.40.590	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type IV / VI secretion system, DotU	0.65	55.0	3.89e-01	94.1%	34.6%
1re0B02	1.10.1000.11	Mainly Alpha › Orthogonal Bundle › Arf Nucleotide-binding Site Opener; domain 2 › Arf Nucleotide-binding Site Opener,domain 2	0.65	55.0	4.32e-01	98.0%	47.0%
3ooqA02	3.20.20.140	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases	0.63	49.0	3.04e-01	82.4%	55.0%
7yq0B01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.61	51.0	3.62e-01	96.1%	42.8%
3dfgA03	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	41.0	4.17e-01	94.1%	85.4%
3io1A01	3.40.630.10	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases	0.52	38.0	2.50e-01	84.3%	49.8%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3500235	621.1.1.0 ↗	alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0.64	53.0	4.64e-01	96.1%	65.0%
4947641	5042.1.1.0 ↗	extended segments › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region	0.64	46.0	4.35e-01	80.4%	69.2%
4580730	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.64	49.0	4.76e-01	96.1%	76.7%
4576399	108.1.1.29 ↗	alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7	0.62	46.0	3.91e-01	80.4%	64.7%
3259377	621.1.1.0 ↗	alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0.62	52.0	4.35e-01	98.0%	73.7%
4011350	309.1.1.0 ↗	a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase	0.62	50.0	3.21e-01	96.1%	59.3%
3722962	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	0.61	48.0	3.01e-01	84.3%	54.3%
5034122	1085.1.1.0 ↗	few secondary structure elements › Archaea X-group 1085 › Archaea H-group 1085.1 › Archaea T-group 1085.1.1	0.61	48.0	4.21e-01	94.1%	69.4%
3615241	75.1.1.1 ↗	beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like › Pro_isomerase	0.60	52.0	3.23e-01	96.1%	64.5%
3643141	101.1.1.121 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-bind_3	0.58	48.0	4.20e-01	94.1%	61.3%

D5 medium residues 653-791

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3u4qB04	6.10.140.1030	Special › Helix non-globular › Helix Hairpins ›	0.68	20.0	2.89e-01	90.6%	52.2%
2lyiA01	1.10.274.60	Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain	0.53	36.0	3.60e-01	98.6%	65.5%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3574087	101.1.10.1 ↗	alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N	0.69	39.0	4.50e-01	87.8%	75.8%
3324665	206.1.1.20 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr	0.50	35.0	2.81e-01	70.5%	47.4%