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RNA-dependent_RNA_polymerase

Euk-Vir

Trichomonas_vaginalis_virus_1

RNA-dependent_RNA_polymerase__YP_009162330__Trichomonas_vaginalis_virus_1__674953

Identity

Accession:: YP_009162330 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

53.2 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 1282-1346

PDB

D2 medium residues 263-329

PDB

D3 medium residues 364-553

PDB

D4 medium residues 898-910_939-1044_1089-1134

PDB

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

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	78.6	6.60e-22	75.1%	24.1%
PF02123.22	RdRP_4	47.8	1.50e-12	28.5%	10.5%

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1mukA02	3.90.1850.10	Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3	0.77	71.0	4.91e-01	98.8%	62.0%
2ztbA03	2.60.40.3040	Mainly Beta › Sandwich › Immunoglobulin-like ›	0.53	16.0	2.85e-01	75.2%	87.5%
2uvaG01	1.20.1050.120	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.51	34.0	3.66e-01	89.7%	79.4%

ECOD (8)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4804033	304.48.1.12 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol	0.72	65.0	4.83e-01	97.0%	80.6%
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	0.71	62.0	4.43e-01	92.1%	49.2%
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	0.71	62.0	4.31e-01	92.1%	44.4%
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	0.65	56.0	4.26e-01	91.5%	59.5%
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	0.65	56.0	4.22e-01	91.5%	57.1%
3960648	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	0.65	56.0	4.55e-01	92.1%	68.9%
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	0.63	54.0	4.24e-01	91.5%	58.8%
3708776	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	0.52	47.0	3.68e-01	95.2%	73.8%

D5 medium residues 911-938_1045-1088

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	35.0	1.20e-08	76.4%	8.6%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3ihjA02	1.10.287.1970	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.66	33.0	4.33e-01	90.3%	92.1%
2elcA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.60	42.0	4.36e-01	93.1%	79.1%
5iduA01	1.10.540.10	Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain	0.56	47.0	3.96e-01	91.7%	63.3%
4muoA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.56	40.0	4.08e-01	97.2%	77.8%
4ga4A01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.56	40.0	4.13e-01	94.4%	82.1%
2pbiA02	1.10.1240.60	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 ›	0.54	37.0	3.27e-01	90.3%	50.5%
5kc8A01	3.40.50.2300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator	0.50	42.0	2.92e-01	91.7%	69.5%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4938198	5054.1.1.0 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels	0.50	33.0	3.14e-01	93.1%	54.4%

D6 medium residues 1135-1198

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02123.22 best	RdRP_4	44.7	1.30e-11	100.0%	15.3%

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1uv7A00	3.30.1360.100	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › General secretion pathway protein M, EpsM	0.66	50.0	4.77e-01	82.8%	88.2%
8a9xA01	3.30.1360.100	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › General secretion pathway protein M, EpsM	0.66	49.0	4.72e-01	82.8%	93.3%
2jheA01	3.30.70.260	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain	0.59	50.0	4.68e-01	100.0%	82.7%
1vx4407	3.30.70.240	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.54	37.0	3.71e-01	76.6%	84.1%
3uc9A00	3.40.50.11960	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold ›	0.53	40.0	3.00e-01	85.9%	83.3%
1kafA00	3.90.1150.20	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription regulator MotA, C-terminal domain	0.50	35.0	3.04e-01	75.0%	67.6%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3927940	304.36.1.2 ↗	a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1	0.67	58.0	4.98e-01	100.0%	82.9%
3935796	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	0.67	59.0	4.34e-01	100.0%	41.8%
3934202	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	0.66	57.0	4.49e-01	100.0%	54.5%
3926633	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	0.66	58.0	4.20e-01	100.0%	37.3%
5076763	304.120.1.6 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer	0.65	47.0	4.52e-01	78.1%	68.0%
3643305	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	0.65	55.0	4.44e-01	100.0%	52.6%
4956226	304.120.1.6 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer	0.64	46.0	4.39e-01	76.6%	66.7%
4981202	310.3.1.0 ↗	a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related	0.59	47.0	4.50e-01	93.8%	77.3%
4870707	4121.1.1.2 ↗	a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like	0.53	42.0	3.00e-01	95.3%	84.9%
3582180	5.1.3.221 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_WDR36-Utp21_1st	0.50	42.0	3.22e-01	100.0%	53.8%
5039664	5.1.5.11 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › PQQ_2	0.50	41.0	2.68e-01	100.0%	30.5%

D7 medium residues 1199-1277

PDB

D8 medium residues 1369-1428

PDB