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RNA-dependent_RNA_polymerase
Euk-VirMedicago_sativa_alphapartitivirus_1
RNA-dependent_RNA_polymerase__YP_009551597__Medicago_sativa_alphapartitivirus_1__2043550
Identity
- Accession:
- YP_009551597 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
81.0
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Duplopiviricetes›
Durnavirales›
Partitiviridae›
Alphapartitivirus›
Medicago_sativa_alphapartitivirus_1
TaxID: 2043550
Cluster
View cluster (450 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
high
residues 105-189
D2
medium
residues 1-22_199-234_351-363
Domain cluster:
representative
CATH (7)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3ib5A00 | 3.10.570.10 | Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain | 0.54 | 38.0 | 2.58e-01 | 77.5% | 40.6% |
| 3jzmA02 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.52 | 37.0 | 2.63e-01 | 77.5% | 78.6% |
| 2g9iA01 | 3.30.1330.100 | Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › CofE-like | 0.51 | 44.0 | 3.63e-01 | 100.0% | 94.2% |
| 4tl8F00 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.51 | 36.0 | 2.66e-01 | 76.1% | 87.8% |
| 5cm2Z00 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.51 | 36.0 | 2.78e-01 | 77.5% | 92.9% |
| 1ixmB02 | 3.30.565.30 | Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Sporulation initiation phosphotransferase B (SpoOB), C-terminal domain | 0.50 | 40.0 | 3.49e-01 | 88.7% | 68.8% |
| 5dvyA02 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.50 | 39.0 | 2.61e-01 | 87.3% | 59.3% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5033908 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.66 | 47.0 | 3.40e-01 | 76.1% | 57.1% |
| 5029815 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.64 | 45.0 | 3.27e-01 | 76.1% | 59.1% |
| 3295391 | 2007.2.3.9 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › PTPlike_phytase | 0.56 | 38.0 | 2.52e-01 | 71.8% | 46.5% |
| 4981955 | 5104.1.1.1 ↗ | a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 | 0.56 | 44.0 | 3.65e-01 | 87.3% | 86.9% |
| 4392521 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.56 | 38.0 | 2.56e-01 | 71.8% | 34.7% |
| 5041727 | 2492.1.1.0 ↗ | a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like | 0.55 | 44.0 | 3.53e-01 | 93.0% | 92.5% |
| 4247735 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.54 | 37.0 | 2.10e-01 | 70.4% | 9.6% |
| 4979109 | 2006.1.4.56 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF5615 | 0.54 | 39.0 | 3.34e-01 | 77.5% | 68.1% |
| 3735731 | 2008.2.1.2 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › Sen15 | 0.53 | 38.0 | 3.17e-01 | 77.5% | 64.7% |
| 4955135 | 2008.1.1.159 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Csa1 | 0.53 | 38.0 | 2.54e-01 | 76.1% | 34.2% |
| 5008124 | 2004.1.1.146 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase | 0.53 | 37.0 | 2.72e-01 | 76.1% | 90.0% |
| 3598626 | 2008.2.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like | 0.51 | 36.0 | 3.41e-01 | 74.6% | 64.4% |
| 5077272 | 2004.1.1.146 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase | 0.51 | 36.0 | 2.59e-01 | 77.5% | 80.7% |
| 3242647 | 2006.1.6.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like | 0.51 | 39.0 | 2.90e-01 | 84.5% | 49.5% |
| 3502215 | 7026.1.1.0 ↗ | beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 | 0.51 | 35.0 | 2.37e-01 | 71.8% | 44.6% |
| 3741335 | 109.4.1.338 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIC1 | 0.51 | 35.0 | 2.36e-01 | 71.8% | 43.7% |
| 3937781 | 2006.1.6.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like | 0.51 | 38.0 | 2.85e-01 | 84.5% | 50.2% |
| 5012532 | 2004.1.1.146 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase | 0.50 | 36.0 | 2.62e-01 | 77.5% | 90.0% |
D3
medium
residues 23-62_456-573
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_656506__Raphanus_sativus_cryptic_virus_1__348449__D32-57_444-535
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2ckwA04 | 1.20.960.20 | Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › | 0.59 | 39.0 | 4.59e-01 | 71.5% | 97.2% |
| 3tahA02 | 1.10.287.1770 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.57 | 29.0 | 3.67e-01 | 70.3% | 83.0% |
| 2xheA04 | 1.25.40.60 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.54 | 30.0 | 3.42e-01 | 72.2% | 71.2% |
| 2afaA00 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.53 | 40.0 | 2.93e-01 | 77.2% | 48.8% |
| 3gt5A00 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.53 | 41.0 | 3.09e-01 | 81.6% | 78.0% |
| 3n3uA00 | 1.10.3290.10 | Mainly Alpha › Orthogonal Bundle › Fic-like fold › Fido-like domain | 0.51 | 39.0 | 3.21e-01 | 93.7% | 43.0% |
D4
medium
residues 63-100_254-295_364-455
Domain cluster:
rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 30.6 | 2.10e-07 | 55.2% | 19.8% |