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putative_RNA-dependent_RNA_polymerase
Euk-VirPanax_notoginseng_virus_B
putative_RNA-dependent_RNA_polymerase__YP_009551937__Panax_notoginseng_virus_B__2248770
Identity
- Accession:
- YP_009551937 ↗
- Protein ID:
- putative_RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
73.2
mean pLDDT
Taxonomy
Orthornavirae›
Duplornaviricota›
Chrymotiviricetes›
Ghabrivirales›
Orthototiviridae›
Totivirus›
Panax_notoginseng_virus_B
TaxID: 2248770
Cluster
View cluster (56 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
medium
residues 34-172_499-523
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009507835__Xanthophyllomyces_dendrorhous_virus_L1B__1167691__D135-271_599-614
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 30.7 | 2.30e-07 | 90.8% | 23.2% |
D2
medium
residues 173-189_216-309_357-411
Domain cluster:
rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 38.0 | 1.40e-09 | 65.1% | 20.9% |
D3
medium
residues 190-215_310-356_412-498
Domain cluster:
rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 75.9 | 4.40e-21 | 54.4% | 17.8% |
| PF02123.22 | RdRP_4 | 22.5 | 7.30e-05 | 39.4% | 11.8% |
D4
medium
residues 524-589
Domain cluster:
representative
CATH (49)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1j8yF01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.70 | 57.0 | 5.16e-01 | 86.4% | 91.9% |
| 4kb2A01 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.70 | 64.0 | 5.35e-01 | 100.0% | 90.8% |
| 4pcqA01 | 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 | 0.69 | 47.0 | 5.15e-01 | 95.5% | 94.0% |
| 1txgA02 | 1.10.1040.10 | Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 | 0.68 | 57.0 | 4.45e-01 | 97.0% | 47.1% |
| 6v7xB02 | 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 | 0.68 | 43.0 | 4.58e-01 | 98.5% | 75.0% |
| 5cvrA02 | 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 | 0.67 | 58.0 | 5.42e-01 | 97.0% | 82.1% |
| 2dbbB01 | 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 | 0.67 | 45.0 | 4.80e-01 | 97.0% | 85.5% |
| 2rn7A01 | 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 | 0.65 | 47.0 | 4.73e-01 | 95.5% | 77.3% |
| 3tgnB02 | 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 | 0.64 | 43.0 | 4.40e-01 | 97.0% | 73.0% |
| 1w0bA01 | 1.20.58.420 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP | 0.64 | 55.0 | 5.01e-01 | 98.5% | 81.5% |
| 4ex8A00 | 3.40.1790.10 | Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain | 0.64 | 44.0 | 2.90e-01 | 72.7% | 16.6% |
| 2qsbA00 | 1.20.1440.50 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like | 0.64 | 50.0 | 4.59e-01 | 89.4% | 65.9% |
| 4asvA00 | 1.20.5.420 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C | 0.64 | 45.0 | 4.25e-01 | 87.9% | 62.0% |
| 4i2oA02 | 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 | 0.64 | 55.0 | 5.22e-01 | 97.0% | 81.2% |
| 1sfxB00 | 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 | 0.63 | 43.0 | 3.75e-01 | 97.0% | 45.2% |
| 3tl4X02 | 1.10.10.2420 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.63 | 49.0 | 4.85e-01 | 97.0% | 81.9% |
| 3d0sA02 | 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 | 0.63 | 54.0 | 5.12e-01 | 97.0% | 85.0% |
| 3dv8A02 | 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 | 0.62 | 53.0 | 5.07e-01 | 100.0% | 82.1% |
| 2gauA02 | 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 | 0.61 | 53.0 | 4.97e-01 | 97.0% | 82.7% |
| 3urzA00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.61 | 49.0 | 3.53e-01 | 89.4% | 49.0% |
| 1o3sA02 | 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 | 0.61 | 53.0 | 5.23e-01 | 97.0% | 97.1% |
| 2xkoA02 | 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 | 0.61 | 53.0 | 4.78e-01 | 100.0% | 75.5% |
| 2om6A02 | 1.10.150.400 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › | 0.61 | 48.0 | 4.57e-01 | 90.9% | 73.4% |
| 4ha8A01 | 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 | 0.61 | 48.0 | 4.96e-01 | 97.0% | 93.7% |
| 3k9tA03 | 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 | 0.60 | 40.0 | 4.00e-01 | 97.0% | 66.7% |
| 2x4hA00 | 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 | 0.60 | 47.0 | 3.82e-01 | 97.0% | 44.2% |
| 1jogA00 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.60 | 47.0 | 3.79e-01 | 86.4% | 86.7% |
| 6l25A00 | 3.20.20.140 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases | 0.60 | 52.0 | 3.48e-01 | 97.0% | 26.3% |
| 2odmA00 | 1.10.287.750 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like | 0.59 | 52.0 | 4.93e-01 | 100.0% | 89.9% |
| 4ev0A02 | 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 | 0.59 | 48.0 | 4.66e-01 | 97.0% | 79.2% |
| 3ibyD02 | 1.10.287.1770 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.59 | 41.0 | 3.86e-01 | 74.2% | 83.3% |
| 4it4A02 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.58 | 45.0 | 4.08e-01 | 84.8% | 69.2% |
| 6f1eA01 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.58 | 50.0 | 3.93e-01 | 97.0% | 50.4% |
| 5dukB00 | 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 | 0.58 | 41.0 | 4.10e-01 | 98.5% | 76.1% |
| 1vmgA00 | 1.10.287.1080 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like | 0.58 | 45.0 | 4.26e-01 | 90.9% | 69.5% |
| 4go1A01 | 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 | 0.57 | 41.0 | 4.44e-01 | 98.5% | 94.4% |
| 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 | 43.0 | 4.22e-01 | 83.3% | 77.0% |
| 2k85A00 | 1.10.10.440 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain | 0.56 | 47.0 | 4.79e-01 | 98.5% | 95.4% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.56 | 43.0 | 4.37e-01 | 95.5% | 83.6% |
| 1j09A05 | 1.10.10.350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.56 | 47.0 | 4.19e-01 | 97.0% | 72.4% |
| 1ft9A02 | 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 | 47.0 | 4.47e-01 | 97.0% | 87.3% |
| 3bh1A02 | 1.20.1570.10 | Mainly Alpha › Up-down Bundle › dip2346 fold › dip2346 domain like | 0.56 | 44.0 | 3.83e-01 | 84.8% | 76.2% |
| 1wi9A01 | 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 | 0.55 | 43.0 | 4.54e-01 | 98.5% | 100.0% |
| 4ijaA01 | 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 | 0.54 | 43.0 | 4.40e-01 | 97.0% | 95.2% |
| 2h09A01 | 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 | 0.53 | 41.0 | 4.04e-01 | 97.0% | 81.7% |
| 2vxzA01 | 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 | 0.53 | 45.0 | 4.53e-01 | 98.5% | 95.5% |
| 1s3jA02 | 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 | 0.52 | 42.0 | 4.28e-01 | 97.0% | 96.9% |
| 3ulqB00 | 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 | 0.51 | 39.0 | 4.11e-01 | 86.4% | 91.4% |
| 3p7nA02 | 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 | 0.50 | 40.0 | 3.90e-01 | 86.4% | 81.9% |
ECOD (27)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3925672 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.74 | 61.0 | 5.78e-01 | 97.0% | 76.2% |
| 3391605 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.69 | 60.0 | 6.05e-01 | 97.0% | 98.5% |
| 4316366 | 1037.1.1.1 ↗ | alpha bundles › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › LGT | 0.69 | 60.0 | 4.26e-01 | 97.0% | 34.0% |
| 5001070 | 1076.1.1.1 ↗ | alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Rce1-like | 0.69 | 61.0 | 4.03e-01 | 100.0% | 65.5% |
| 4982322 | 5081.1.1.1 ↗ | alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid | 0.68 | 61.0 | 4.19e-01 | 98.5% | 51.8% |
| 3383195 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.67 | 57.0 | 4.00e-01 | 97.0% | 82.7% |
| 3965260 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.65 | 51.0 | 4.74e-01 | 86.4% | 91.8% |
| 3391717 | 101.1.1.112 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg | 0.65 | 51.0 | 4.68e-01 | 95.5% | 64.4% |
| 4964648 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.64 | 54.0 | 3.78e-01 | 98.5% | 68.1% |
| 5007466 | 159.1.2.2 ↗ | alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG | 0.64 | 47.0 | 4.23e-01 | 80.3% | 56.7% |
| 3408065 | 101.1.1.112 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg | 0.64 | 54.0 | 4.88e-01 | 98.5% | 93.7% |
| None | — | 0.63 | 54.0 | 5.15e-01 | 100.0% | 83.1% | |
| 3860590 | 101.1.1.101 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › HTH_40 | 0.63 | 42.0 | 4.55e-01 | 97.0% | 92.0% |
| 3922872 | 101.1.1.112 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg | 0.63 | 54.0 | 4.83e-01 | 98.5% | 92.6% |
| 4241641 | 140.1.1.7 ↗ | alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_2 | 0.62 | 45.0 | 3.84e-01 | 86.4% | 45.2% |
| 3219867 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.62 | 48.0 | 4.42e-01 | 83.3% | 70.6% |
| 3776363 | 873.1.1.5 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB | 0.62 | 52.0 | 3.67e-01 | 95.5% | 32.1% |
| 5043220 | 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 | 0.62 | 51.0 | 4.73e-01 | 92.4% | 98.8% |
| 3806239 | 616.1.1.0 ↗ | alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain | 0.61 | 50.0 | 4.83e-01 | 93.9% | 85.3% |
| 3270287 | 3877.1.1.1 ↗ | alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP | 0.58 | 51.0 | 3.53e-01 | 98.5% | 55.9% |
| 3321233 | 604.12.1.2 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 | 0.58 | 44.0 | 4.10e-01 | 84.8% | 65.9% |
| 3668118 | 604.12.1.2 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 | 0.58 | 45.0 | 4.33e-01 | 87.9% | 72.5% |
| 3590053 | 633.21.1.0 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 | 0.57 | 43.0 | 4.03e-01 | 83.3% | 71.8% |
| 3969664 | 101.1.1.18 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › HTH_8 | 0.55 | 42.0 | 4.17e-01 | 98.5% | 77.9% |
| 5030299 | 633.16.1.0 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like | 0.55 | 46.0 | 4.35e-01 | 92.4% | 92.5% |
| 3938318 | 4992.1.1.0 ↗ | extended segments › RelB-like › RelB-like › RelB-like | 0.51 | 46.0 | 3.77e-01 | 100.0% | 95.0% |
| 4895784 | 101.1.2.623 ↗ | alpha arrays › HTH › HTH › winged helix domain › PF25983 | 0.50 | 38.0 | 3.81e-01 | 100.0% | 83.6% |
D5
medium
residues 597-737