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RNA-dependent_RNA-polymerase

Euk-Vir

Elderberry_latent_virus

RNA-dependent_RNA-polymerase__YP_009116634__Elderberry_latent_virus__167018

Identity

Accession:: YP_009116634 ↗
Protein ID:: RNA-dependent_RNA-polymerase
Kingdom:: euk

Quality

79.4 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Tolucaviricetes› Tolivirales› Tombusviridae› Pelarspovirus› Elderberry_latent_virus

TaxID: 167018

Cluster

View cluster (58 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 612-742

PDB

Domain cluster: rep: P95_replicase__YP_009259667__Pelargonium_leaf_curl_virus__35280__D527-559_693-852

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	102.9	2.70e-29	99.2%	27.4%

D2 medium residues 1-58

PDB

D3 medium residues 80-183

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF08500.17 best	Tombus_P33	34.1	4.70e-08	92.3%	60.0%

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3kh1A00	1.10.3210.10	Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432	0.60	45.0	3.69e-01	79.8%	73.8%
2og9A01	3.30.390.10	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain	0.59	41.0	3.80e-01	71.2%	62.3%
2dodA00	1.10.10.440	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain	0.59	41.0	4.43e-01	99.0%	91.5%
2i2xB01	1.10.1240.10	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain	0.56	38.0	3.93e-01	70.2%	94.0%
2mqaA00	1.10.274.60	Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain	0.54	38.0	3.60e-01	94.2%	60.8%
3fbzA01	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.53	37.0	3.82e-01	86.5%	75.5%
7e5aB02	1.20.1000.10	Mainly Alpha › Up-down Bundle › Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 › Guanylate-binding protein, C-terminal domain	0.52	42.0	3.66e-01	92.3%	56.7%
4v1gA00	1.20.20.10	Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C	0.51	28.0	3.09e-01	71.2%	64.7%
2wzkA03	1.20.1310.10	Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats	0.51	43.0	4.27e-01	95.2%	94.5%
2pq7A00	1.10.3210.10	Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432	0.50	45.0	3.81e-01	100.0%	76.3%
2odmA00	1.10.287.750	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like	0.50	34.0	3.78e-01	84.6%	91.1%

ECOD (17)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3952621	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.74	48.0	5.68e-01	90.4%	98.6%
4124450	101.35.1.4 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3	0.73	47.0	5.57e-01	90.4%	100.0%
4396592	7064.1.1.3 ↗	alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › FUSC_2	0.71	47.0	4.19e-01	89.4%	47.3%
4093848	3584.1.1.1 ↗	alpha arrays › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA_pol3_finger	0.66	45.0	3.59e-01	70.2%	43.8%
1211456	610.3.1.2 ↗	alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › tRNA_synt_1c_R2,tRNA_synt_1c_R1	0.66	52.0	4.25e-01	83.7%	58.1%
3170802	101.1.1.133 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Vhr1	0.63	45.0	4.71e-01	74.0%	84.2%
3171699	101.1.1.133 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Vhr1	0.63	44.0	4.56e-01	73.1%	80.0%
3530124	386.1.1.0 ↗	few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers	0.63	38.0	4.28e-01	88.5%	78.8%
4943037	101.1.17.1 ↗	alpha arrays › HTH › HTH › FF domain › Ribosomal_S17e	0.59	39.0	4.40e-01	70.2%	92.0%
4014527	532.2.1.0 ↗	alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains	0.59	47.0	4.93e-01	94.2%	95.8%
5029167	206.1.1.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase	0.57	47.0	3.45e-01	87.5%	39.8%
3167160	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.57	43.0	2.76e-01	80.8%	42.0%
3492885	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.57	39.0	4.27e-01	71.2%	95.0%
4028766	181.1.1.1 ↗	alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N	0.52	36.0	3.84e-01	91.3%	83.3%
3789554	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.51	39.0	4.18e-01	98.1%	93.3%
None	—		0.51	45.0	3.21e-01	98.1%	81.3%
3929607	106.1.1.0 ↗	alpha arrays › Globin-like › Globin-like › Globin-like	0.50	43.0	3.68e-01	94.2%	93.5%

D4 medium residues 423-476_527-611

PDB

Domain cluster: rep: hypothetical_protein_1__YP_009337274__Changjiang_tombus-like_virus_14__1922807__D158-196_253-344

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	103.5	1.70e-29	61.9%	17.3%
PF00998.29	RdRP_3	76.3	3.00e-21	38.9%	11.1%