←Back to structures
RNA-directed_RNA_polymerase_nsp4
Euk-VirMadariaga_virus
RNA-directed_RNA_polymerase_nsp4__YP_009020586__Madariaga_virus__1440170
Identity
- Accession:
- YP_009020586 ↗
- Protein ID:
- RNA-directed_RNA_polymerase_nsp4
- Kingdom:
- euk
Quality
89.0
mean pLDDT
Taxonomy
Orthornavirae›
Kitrinoviricota›
Alsuviricetes›
Martellivirales›
Togaviridae›
Alphavirus›
Madariaga_virus
TaxID: 1440170
Cluster
View cluster (32 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 35-90
Domain cluster:
representative
CATH (23)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1a36A04 | 1.10.132.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › | 0.92 | 78.0 | 5.28e-01 | 89.3% | 37.7% |
| 2yfaA02 | 1.20.1440.210 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.89 | 70.0 | 5.35e-01 | 82.1% | 41.4% |
| 2ic6A00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.89 | 75.0 | 6.83e-01 | 89.3% | 77.5% |
| 8fbnB01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.86 | 72.0 | 4.67e-01 | 89.3% | 39.6% |
| 4iggA01 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.86 | 68.0 | 6.44e-01 | 85.7% | 79.1% |
| 6r1nA01 | 1.10.287.40 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain | 0.86 | 69.0 | 5.60e-01 | 87.5% | 56.3% |
| 1hr5A00 | 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 | 0.84 | 61.0 | 6.53e-01 | 76.8% | 95.8% |
| 4w8pA02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.83 | 66.0 | 4.97e-01 | 85.7% | 38.5% |
| 4e4eA01 | 1.10.287.990 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain | 0.80 | 65.0 | 6.01e-01 | 89.3% | 78.9% |
| 3dyjA02 | 1.20.1420.10 | Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain | 0.80 | 62.0 | 4.54e-01 | 85.7% | 33.1% |
| 2e9xA01 | 1.20.58.1030 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.80 | 68.0 | 5.18e-01 | 94.6% | 68.0% |
| 1tjoB00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.77 | 68.0 | 4.65e-01 | 94.6% | 62.9% |
| 1ku9A02 | 1.10.287.450 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin | 0.77 | 61.0 | 5.90e-01 | 87.5% | 85.9% |
| 1cpyA02 | 1.10.287.410 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.76 | 56.0 | 5.13e-01 | 80.4% | 61.1% |
| 1vq8V00 | 1.10.287.310 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.74 | 59.0 | 5.63e-01 | 87.5% | 92.3% |
| 1wrdA00 | 1.20.58.160 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.71 | 57.0 | 4.82e-01 | 91.1% | 76.5% |
| 5ffdA00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.68 | 54.0 | 4.22e-01 | 92.9% | 73.7% |
| 1wkbA03 | 1.10.730.10 | Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 | 0.68 | 51.0 | 3.99e-01 | 80.4% | 51.2% |
| 4j8dD00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.66 | 51.0 | 3.67e-01 | 83.9% | 96.9% |
| 4ksaA02 | 1.20.140.90 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain | 0.63 | 53.0 | 3.96e-01 | 91.1% | 73.7% |
| 2lpeA01 | 6.10.140.1120 | Special › Helix non-globular › Helix Hairpins › | 0.62 | 50.0 | 4.59e-01 | 92.9% | 76.9% |
| 2ggfA00 | 1.25.40.180 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.62 | 46.0 | 3.47e-01 | 80.4% | 37.2% |
| 4u1cA01 | 4.10.860.10 | Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain | 0.60 | 41.0 | 4.27e-01 | 73.2% | 78.8% |
ECOD (36)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3215082 | 4177.1.1.0 ↗ | alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like | 0.92 | 74.0 | 5.41e-01 | 85.7% | 39.3% |
| 3646879 | 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 | 0.91 | 66.0 | 4.62e-01 | 76.8% | 28.1% |
| 3503444 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.89 | 75.0 | 6.26e-01 | 89.3% | 62.2% |
| 4201121 | 192.7.1.0 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm | 0.89 | 73.0 | 7.16e-01 | 87.5% | 90.0% |
| 3320767 | 150.1.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin | 0.89 | 78.0 | 5.34e-01 | 94.6% | 33.7% |
| 3959306 | 150.8.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE | 0.89 | 72.0 | 5.21e-01 | 87.5% | 35.2% |
| 3170937 | 4177.1.1.1 ↗ | alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH | 0.88 | 71.0 | 4.40e-01 | 85.7% | 18.9% |
| 4955279 | 5082.1.1.1 ↗ | alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux | 0.88 | 74.0 | 4.88e-01 | 89.3% | 29.5% |
| 3853063 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.86 | 70.0 | 5.36e-01 | 87.5% | 45.8% |
| 5077923 | 5082.1.1.1 ↗ | alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux | 0.86 | 77.0 | 5.20e-01 | 96.4% | 64.3% |
| 3781156 | 109.4.1.70 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CID | 0.85 | 59.0 | 3.88e-01 | 73.2% | 20.9% |
| 3590461 | 5050.1.1.50 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › DUF1275 | 0.85 | 76.0 | 5.03e-01 | 100.0% | 87.9% |
| 4927816 | 5082.1.1.1 ↗ | alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux | 0.85 | 75.0 | 4.93e-01 | 96.4% | 67.1% |
| 4045999 | 5082.1.1.1 ↗ | alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux | 0.84 | 74.0 | 4.96e-01 | 96.4% | 67.5% |
| 4488200 | 604.12.1.0 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain | 0.84 | 71.0 | 5.67e-01 | 92.9% | 81.7% |
| 4501359 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.84 | 72.0 | 5.46e-01 | 92.9% | 68.8% |
| 5032752 | 5069.1.3.0 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits | 0.83 | 72.0 | 6.17e-01 | 92.9% | 63.5% |
| 3264784 | 2003.1.1.0 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains | 0.82 | 76.0 | 4.39e-01 | 100.0% | 39.6% |
| 3556027 | 5086.1.1.0 ↗ | alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins | 0.82 | 67.0 | 5.80e-01 | 89.3% | 64.7% |
| 3855461 | 3922.1.1.0 ↗ | alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 | 0.82 | 67.0 | 5.79e-01 | 89.3% | 64.7% |
| 5039785 | 632.22.1.200 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › PF26119 | 0.82 | 73.0 | 6.00e-01 | 96.4% | 64.9% |
| 3180581 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.81 | 70.0 | 5.99e-01 | 92.9% | 65.9% |
| 3258925 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.81 | 65.0 | 6.07e-01 | 87.5% | 78.6% |
| 4979634 | 4163.1.1.1 ↗ | alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 | 0.81 | 67.0 | 5.31e-01 | 92.9% | 61.7% |
| 5054469 | 192.7.1.2 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N | 0.81 | 65.0 | 5.25e-01 | 87.5% | 52.4% |
| 3574188 | 601.33.1.8 ↗ | alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › Frag1 | 0.80 | 69.0 | 4.97e-01 | 92.9% | 44.8% |
| 5002089 | 2004.1.1.144 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD_2 | 0.79 | 65.0 | 3.99e-01 | 89.3% | 16.5% |
| 5010044 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.79 | 64.0 | 5.42e-01 | 91.1% | 61.1% |
| 1203190 | 192.3.1.1 ↗ | alpha bundles › Long alpha-hairpin › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Sod_Fe_N | 0.79 | 63.0 | 5.38e-01 | 89.3% | 60.2% |
| 5008319 | 605.1.1.10 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › SPOB_a | 0.79 | 62.0 | 5.96e-01 | 87.5% | 78.5% |
| 4946791 | 605.1.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase | 0.78 | 61.0 | 5.59e-01 | 85.7% | 68.0% |
| 5077382 | 192.7.1.0 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm | 0.74 | 64.0 | 5.37e-01 | 96.4% | 87.4% |
| 3245538 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.73 | 60.0 | 4.96e-01 | 92.9% | 81.9% |
| 4961508 | 605.1.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase | 0.72 | 56.0 | 5.18e-01 | 87.5% | 69.3% |
| 3606020 | 5054.1.1.0 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels | 0.70 | 60.0 | 3.84e-01 | 92.9% | 43.1% |
| 3203002 | 109.4.1.2832 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › mTOR_dom, HEAT_EZ, TPR_IMB1 | 0.62 | 52.0 | 2.80e-01 | 100.0% | 83.8% |
D2
medium
residues 106-134_342-360_511-608
Domain cluster:
rep: replication_protein_2a__YP_006576519__Amazon_lily_mild_mottle_virus__1195163__D529-657
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 40.8 | 1.80e-10 | 80.8% | 20.0% |
D3
medium
residues 216-293_305-341_379-459
Domain cluster:
rep: ORF_1b__YP_003289291__Strawberry_pallidosis-associated_virus__227507__D117-174_213-235_276-309
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 82.9 | 3.30e-23 | 59.2% | 27.1% |
| PF00978.27 | RdRP_2 | 46.3 | 4.10e-12 | 40.8% | 16.6% |
D4
medium
residues 361-378_460-510
Domain cluster:
rep: nsP4_protein__NP_740652__Eastern_equine_encephalitis_virus__11021__D358-385_493-514
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 54.3 | 1.50e-14 | 75.4% | 10.7% |