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putative_RNA-dependent_RNA_polymerase
Euk-VirPepper_cryptic_virus_1
putative_RNA-dependent_RNA_polymerase__YP_009466859__Pepper_cryptic_virus_1__369643
Identity
- Accession:
- YP_009466859 ↗
- Protein ID:
- putative_RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
87.8
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Duplopiviricetes›
Durnavirales›
Partitiviridae›
Deltapartitivirus›
Pepper_cryptic_virus_1
TaxID: 369643
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 40-63_407-475
Domain cluster:
rep: RdRp__YP_009329866__Wuhan_large_pig_roundworm_virus_1__1923741__D24-47_379-435
D2
medium
residues 66-82_179-212_266-317
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 27.1 | 2.40e-06 | 51.5% | 11.1% |
| PF00680.26 | RdRP_1 | 27.3 | 2.10e-06 | 49.5% | 11.1% |
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1neiA00 | 3.30.160.220 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YoaG | 0.59 | 26.0 | 3.31e-01 | 78.6% | 70.0% |
| 6c1qB02 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.53 | 43.0 | 3.25e-01 | 91.3% | 81.4% |
| 3d36B02 | 1.10.287.130 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain | 0.53 | 28.0 | 3.48e-01 | 93.2% | 85.2% |
| 2w00A02 | 3.90.640.50 | Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › | 0.52 | 31.0 | 3.52e-01 | 90.3% | 80.8% |
| 5e1wA00 | 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 | 35.0 | 3.07e-01 | 72.8% | 91.1% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3236725 | 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 | 0.67 | 52.0 | 3.88e-01 | 83.5% | 52.7% |
| 3960648 | 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 | 0.66 | 51.0 | 3.66e-01 | 83.5% | 48.5% |
| 3175336 | 376.1.1.0 ↗ | few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box | 0.64 | 30.0 | 3.43e-01 | 84.5% | 60.0% |
| 3994884 | 5001.1.1.0 ↗ | alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like | 0.50 | 41.0 | 3.00e-01 | 91.3% | 75.8% |
D3
medium
residues 83-106_213-265_318-406
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 |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 64.5 | 1.10e-17 | 53.6% | 22.0% |
| PF00680.26 | RdRP_1 | 33.8 | 2.20e-08 | 34.9% | 12.2% |
CATH (17)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6qwtA02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.83 | 64.0 | 6.97e-01 | 79.5% | 97.9% |
| 1gx5A03 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.81 | 59.0 | 6.83e-01 | 83.1% | 100.0% |
| 5jxsA02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.81 | 63.0 | 6.87e-01 | 80.7% | 97.9% |
| 1hi8A03 | 3.30.70.1600 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.71 | 58.0 | 5.72e-01 | 85.5% | 93.2% |
| 7uinD01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.66 | 56.0 | 5.66e-01 | 89.8% | 99.4% |
| 4ol8A01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.64 | 44.0 | 4.85e-01 | 98.8% | 86.7% |
| 3n28A02 | 3.30.70.2020 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.62 | 35.0 | 4.24e-01 | 89.8% | 85.8% |
| 3hvwA00 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.60 | 43.0 | 4.39e-01 | 73.5% | 86.8% |
| 3pjxA01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.59 | 47.0 | 4.58e-01 | 82.5% | 84.5% |
| 1qltA03 | 3.40.462.10 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain | 0.58 | 45.0 | 4.02e-01 | 81.3% | 74.9% |
| 5fxdA03 | 3.40.462.10 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain | 0.57 | 44.0 | 3.91e-01 | 80.1% | 74.2% |
| 1q8iA04 | 3.90.1600.10 | Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain | 0.56 | 45.0 | 4.22e-01 | 85.5% | 76.6% |
| 3aawA02 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.55 | 38.0 | 3.88e-01 | 70.5% | 84.8% |
| 4zmuA02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.55 | 43.0 | 4.50e-01 | 85.5% | 89.0% |
| 5o60I00 | 3.30.70.1730 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain | 0.53 | 36.0 | 4.07e-01 | 74.1% | 91.3% |
| 1ac1A00 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.51 | 34.0 | 3.28e-01 | 92.8% | 58.5% |
| 3lwsF02 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.50 | 30.0 | 3.70e-01 | 70.5% | 95.2% |
ECOD (26)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| None | — | 0.87 | 77.0 | 5.73e-01 | 91.0% | 82.2% | |
| 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 | 0.87 | 76.0 | 5.66e-01 | 91.0% | 83.3% |
| 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 | 0.87 | 77.0 | 5.73e-01 | 91.6% | 82.4% |
| 1789314 | 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 | 74.0 | 5.38e-01 | 91.0% | 74.9% |
| 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 | 0.82 | 77.0 | 5.83e-01 | 98.2% | 87.4% |
| 4152428 | 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 | 0.70 | 57.0 | 4.42e-01 | 85.5% | 56.9% |
| 3630469 | 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 | 0.69 | 56.0 | 4.48e-01 | 85.5% | 80.6% |
| 4296494 | 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 | 0.69 | 56.0 | 4.54e-01 | 85.5% | 79.3% |
| 5002351 | 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 | 0.68 | 57.0 | 4.36e-01 | 89.2% | 90.1% |
| 3068775 | 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 | 0.68 | 55.0 | 5.13e-01 | 84.9% | 85.7% |
| 3939861 | 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 | 0.67 | 48.0 | 5.47e-01 | 77.7% | 100.0% |
| 3483524 | 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 | 0.67 | 54.0 | 4.43e-01 | 85.5% | 64.3% |
| 4890630 | 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 | 0.64 | 52.0 | 4.59e-01 | 85.5% | 75.3% |
| 4982806 | 304.20.1.4 ↗ | a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C | 0.64 | 45.0 | 4.34e-01 | 71.1% | 96.8% |
| 3170846 | 304.60.1.12 ↗ | a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › PF29803 | 0.62 | 45.0 | 4.19e-01 | 74.7% | 90.0% |
| 3907339 | 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 | 0.62 | 46.0 | 3.99e-01 | 76.5% | 65.3% |
| 4116969 | 304.48.1.14 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF | 0.61 | 48.0 | 4.51e-01 | 82.5% | 79.0% |
| 135348 | 304.48.1.14 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF | 0.60 | 43.0 | 4.39e-01 | 73.5% | 86.8% |
| 3931851 | 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 | 53.0 | 4.51e-01 | 100.0% | 87.9% |
| 3937211 | 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 | 0.55 | 51.0 | 4.31e-01 | 100.0% | 84.4% |
| 3925602 | 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 | 0.55 | 51.0 | 4.36e-01 | 100.0% | 86.9% |
| 3936323 | 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 | 0.54 | 50.0 | 4.36e-01 | 100.0% | 85.7% |
| 4096485 | 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 | 0.53 | 49.0 | 4.21e-01 | 100.0% | 89.2% |
| 3742864 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.52 | 34.0 | 4.03e-01 | 76.5% | 97.3% |
| 5026064 | 304.1.1.1 ↗ | a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C | 0.51 | 29.0 | 3.44e-01 | 72.9% | 83.8% |
| 3713158 | 304.60.1.2 ↗ | a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 | 0.50 | 38.0 | 3.46e-01 | 77.1% | 60.3% |
D4
medium
residues 107-178
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009508068__Beet_cryptic_virus_2__912029__D122-174