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putative_RNA-dependent_RNA_polymerase
Euk-VirGrapevine_deformation_virus
putative_RNA-dependent_RNA_polymerase__YP_006347732__Grapevine_deformation_virus__233784
Identity
- Accession:
- YP_006347732 ↗
- Protein ID:
- putative_RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
75.9
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Pisoniviricetes›
Picornavirales›
Secoviridae›
Nepovirus›
Grapevine_deformation_virus
TaxID: 233784
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 540-681
D2
medium
residues 1-242_279-331
Domain cluster:
rep: RNA-dependent_RNA-polymerase_-RdRp-__YP_004429254__Grapevine_Bulgarian_latent_virus__748667__D66-229_264-320
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 54.3 | 1.40e-14 | 67.5% | 41.8% |
ECOD (12)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5367 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.84 | 78.0 | 7.05e-01 | 95.6% | 78.0% |
| 2541763 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.82 | 76.0 | 6.93e-01 | 95.6% | 77.9% |
| 1173784 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.81 | 75.0 | 6.87e-01 | 95.6% | 77.5% |
| None | — | 0.80 | 75.0 | 6.86e-01 | 95.6% | 77.6% | |
| 1875037 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.80 | 76.0 | 6.80e-01 | 98.0% | 77.1% |
| 4871000 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.78 | 66.0 | 7.01e-01 | 86.8% | 99.2% |
| 1279063 | 304.48.1.13 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 | 0.75 | 73.0 | 6.22e-01 | 100.0% | 73.2% |
| 217141 | 304.48.1.15 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 | 0.72 | 63.0 | 5.86e-01 | 95.9% | 74.5% |
| 5366 | 304.48.1.15 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 | 0.72 | 62.0 | 5.56e-01 | 89.8% | 69.6% |
| 4875416 | 304.48.1.13 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 | 0.71 | 62.0 | 5.59e-01 | 92.2% | 68.4% |
| 3691350 | 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 | 0.63 | 50.0 | 5.22e-01 | 80.7% | 89.6% |
| 4361688 | 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 | 0.57 | 48.0 | 4.40e-01 | 89.5% | 67.7% |
D3
medium
residues 445-523
Domain cluster:
representative
CATH (33)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2gs4A00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.75 | 54.0 | 4.28e-01 | 75.9% | 89.9% |
| 3k9iA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.75 | 57.0 | 5.19e-01 | 87.3% | 62.1% |
| 7nazA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.72 | 60.0 | 4.08e-01 | 98.7% | 25.8% |
| 2j4bB00 | 1.25.40.500 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › TFIID subunit TAF5, NTD2 domain | 0.70 | 59.0 | 4.99e-01 | 93.7% | 67.7% |
| 1vb5A01 | 1.20.120.420 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 | 0.69 | 56.0 | 5.36e-01 | 89.9% | 87.2% |
| 2oerA00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.69 | 51.0 | 3.89e-01 | 77.2% | 65.4% |
| 4dmvA01 | 1.20.58.1190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.68 | 48.0 | 4.76e-01 | 75.9% | 78.8% |
| 1hu3A00 | 1.25.40.180 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.67 | 53.0 | 4.00e-01 | 87.3% | 41.2% |
| 2kckA00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.67 | 53.0 | 4.69e-01 | 89.9% | 59.8% |
| 3oxfA05 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.66 | 48.0 | 4.91e-01 | 77.2% | 84.0% |
| 2j49A00 | 1.25.40.500 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › TFIID subunit TAF5, NTD2 domain | 0.65 | 56.0 | 4.71e-01 | 94.9% | 67.9% |
| 1hz4A00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.65 | 53.0 | 3.45e-01 | 89.9% | 20.5% |
| 4u2xF00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.65 | 51.0 | 3.98e-01 | 86.1% | 53.1% |
| 3bqoA00 | 1.25.40.210 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Telomere repeat-binding factor, dimerisation domain | 0.65 | 55.0 | 4.13e-01 | 96.2% | 44.6% |
| 4kn7D01 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.64 | 46.0 | 3.92e-01 | 75.9% | 81.2% |
| 4flbA00 | 1.25.40.90 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.64 | 51.0 | 4.42e-01 | 89.9% | 58.0% |
| 4y97D00 | 1.10.3200.20 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › DNA Polymerase alpha, zinc finger | 0.64 | 49.0 | 3.82e-01 | 83.5% | 94.4% |
| 4g80T00 | 1.20.120.350 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C | 0.63 | 45.0 | 3.80e-01 | 75.9% | 64.7% |
| 3rkvA00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.62 | 51.0 | 4.22e-01 | 91.1% | 72.8% |
| 4i9cA02 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.62 | 54.0 | 4.00e-01 | 100.0% | 82.8% |
| 2qgmA03 | 1.20.1440.30 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Biosynthetic Protein domain | 0.61 | 44.0 | 3.92e-01 | 75.9% | 54.3% |
| 2diwA01 | 1.25.40.90 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.60 | 49.0 | 4.10e-01 | 89.9% | 65.2% |
| 2dbaA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.60 | 49.0 | 4.35e-01 | 91.1% | 77.1% |
| 1vkeB00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.60 | 52.0 | 4.79e-01 | 98.7% | 76.2% |
| 2a9uA01 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.59 | 44.0 | 3.79e-01 | 79.7% | 59.5% |
| 3wirA02 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.57 | 49.0 | 3.21e-01 | 100.0% | 86.8% |
| 2fonA04 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.55 | 41.0 | 3.56e-01 | 81.0% | 54.3% |
| 2np3A00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.55 | 44.0 | 3.81e-01 | 96.2% | 71.1% |
| 2q00B00 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.53 | 39.0 | 3.43e-01 | 78.5% | 74.6% |
| 3cllA00 | 1.20.1080.10 | Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. | 0.52 | 43.0 | 3.19e-01 | 96.2% | 94.6% |
| 3u9jA00 | 1.20.120.520 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like | 0.52 | 45.0 | 3.66e-01 | 98.7% | 93.6% |
| 1um8A01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.51 | 44.0 | 3.25e-01 | 100.0% | 67.0% |
| 2i53A01 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.50 | 42.0 | 3.56e-01 | 96.2% | 60.1% |
ECOD (27)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3872918 | 109.4.1.1286 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_12 | 0.73 | 59.0 | 4.28e-01 | 87.3% | 39.1% |
| 3410683 | 4320.1.1.1 ↗ | alpha superhelices › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › TFIID_NTD2 | 0.73 | 64.0 | 5.14e-01 | 98.7% | 58.7% |
| 3598195 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.72 | 59.0 | 4.83e-01 | 88.6% | 54.3% |
| 3318512 | 109.4.1.420 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR | 0.71 | 58.0 | 4.80e-01 | 88.6% | 50.7% |
| 3651413 | 109.4.1.1256 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 | 0.71 | 65.0 | 4.51e-01 | 100.0% | 86.1% |
| 3614236 | 109.4.1.218 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SNAP | 0.71 | 60.0 | 4.10e-01 | 94.9% | 51.9% |
| 3347410 | 109.4.1.189 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 | 0.71 | 59.0 | 4.90e-01 | 89.9% | 52.6% |
| 3895604 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.70 | 58.0 | 4.55e-01 | 88.6% | 63.1% |
| 3722903 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.70 | 56.0 | 4.01e-01 | 87.3% | 37.6% |
| 3638893 | 4320.1.1.1 ↗ | alpha superhelices › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › TFIID_NTD2 | 0.70 | 59.0 | 4.40e-01 | 92.4% | 46.2% |
| 3211680 | 109.7.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E | 0.70 | 56.0 | 5.40e-01 | 87.3% | 85.6% |
| 4667651 | 4320.1.1.1 ↗ | alpha superhelices › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › TFIID_NTD2 | 0.69 | 59.0 | 4.90e-01 | 94.9% | 65.0% |
| 5075584 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.68 | 54.0 | 4.18e-01 | 86.1% | 52.0% |
| 3427778 | 604.1.1.144 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF26575 | 0.67 | 46.0 | 4.62e-01 | 70.9% | 95.0% |
| 3659378 | 109.4.1.1273 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3 | 0.67 | 61.0 | 4.12e-01 | 98.7% | 61.5% |
| 3366338 | 109.4.1.1277 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, TPR_24 | 0.67 | 55.0 | 4.29e-01 | 94.9% | 42.7% |
| 3950687 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.67 | 54.0 | 4.82e-01 | 89.9% | 66.1% |
| 3962147 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.67 | 58.0 | 3.99e-01 | 100.0% | 52.8% |
| 3342039 | 109.4.1.189 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 | 0.66 | 50.0 | 4.40e-01 | 86.1% | 54.8% |
| 2672579 | 109.4.1.275 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Rgg_C | 0.66 | 58.0 | 4.31e-01 | 100.0% | 56.5% |
| 1789315 | 4967.1.1.0 ↗ | alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases | 0.66 | 54.0 | 4.65e-01 | 92.4% | 78.5% |
| None | — | 0.65 | 49.0 | 3.30e-01 | 81.0% | 26.2% | |
| 3903775 | 192.8.1.419 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › PF27603 | 0.64 | 46.0 | 4.06e-01 | 75.9% | 78.3% |
| 3184857 | 611.3.1.0 ↗ | alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | 0.63 | 50.0 | 3.75e-01 | 88.6% | 56.3% |
| 3299763 | 109.4.1.1262 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_long | 0.63 | 53.0 | 3.53e-01 | 93.7% | 42.8% |
| 3208903 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.60 | 50.0 | 3.16e-01 | 94.9% | 22.3% |
| 4306177 | 2003.1.1.0 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains | 0.58 | 47.0 | 3.14e-01 | 93.7% | 58.9% |