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RNA-dependent_RNA_polymerase
Euk-VirRed_clover_cryptic_virus_1
RNA-dependent_RNA_polymerase__YP_008719882__Red_clover_cryptic_virus_1__1408894
Identity
- Accession:
- YP_008719882 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
81.0
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Duplopiviricetes›
Durnavirales›
Partitiviridae›
Red_clover_cryptic_virus_1
TaxID: 1408894
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 38-70_495-609
D2
high
residues 401-486
Domain cluster:
rep: ORF2__YP_004581250__Piscine_myocarditis_virus_AL_V-708__912320__D347-428
CATH (43)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1ra6A02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.80 | 67.0 | 6.23e-01 | 91.9% | 71.7% |
| 6qwtA02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.79 | 71.0 | 5.94e-01 | 98.8% | 58.9% |
| 5jxsA02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.77 | 70.0 | 5.85e-01 | 98.8% | 59.2% |
| 4tqrA01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.73 | 59.0 | 5.71e-01 | 97.7% | 77.6% |
| 1qf6A02 | 3.30.980.10 | Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 | 0.66 | 58.0 | 5.40e-01 | 96.5% | 86.8% |
| 3pjxA01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.66 | 57.0 | 4.55e-01 | 97.7% | 57.5% |
| 2nyiA01 | 3.30.70.260 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain | 0.66 | 49.0 | 5.08e-01 | 88.4% | 85.2% |
| 3cjeA00 | 3.30.300.20 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain | 0.66 | 50.0 | 4.16e-01 | 81.4% | 59.3% |
| 4r0mA02 | 3.30.300.30 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain | 0.65 | 57.0 | 5.32e-01 | 97.7% | 97.2% |
| 2yx1A01 | 3.30.70.2580 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.64 | 41.0 | 4.49e-01 | 86.0% | 83.3% |
| 6pwjA01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.64 | 55.0 | 4.52e-01 | 97.7% | 56.4% |
| 5ey9A01 | 3.30.300.30 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain | 0.62 | 55.0 | 4.89e-01 | 98.8% | 96.0% |
| 2cg8B02 | 3.30.70.560 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK | 0.62 | 55.0 | 4.78e-01 | 98.8% | 72.7% |
| 1utaA00 | 3.30.70.1070 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat | 0.62 | 45.0 | 4.73e-01 | 87.2% | 85.7% |
| 1ib8A01 | 3.30.300.70 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › RimP-like superfamily, N-terminal | 0.61 | 48.0 | 4.96e-01 | 87.2% | 100.0% |
| 2lkiA00 | 1.10.1200.10 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like | 0.60 | 48.0 | 4.90e-01 | 93.0% | 90.4% |
| 8dq6A01 | 3.30.429.10 | Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor | 0.60 | 49.0 | 4.73e-01 | 90.7% | 91.0% |
| 3nx3A01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.60 | 45.0 | 3.88e-01 | 100.0% | 49.6% |
| 6erkA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.60 | 44.0 | 3.71e-01 | 100.0% | 43.4% |
| 7nasX01 | 3.30.300.70 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › RimP-like superfamily, N-terminal | 0.60 | 49.0 | 5.07e-01 | 89.5% | 100.0% |
| 4w1vA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.59 | 43.0 | 3.65e-01 | 100.0% | 43.7% |
| 2lqjA00 | 3.30.70.260 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain | 0.58 | 47.0 | 4.61e-01 | 90.7% | 83.0% |
| 3laxA00 | 3.30.300.30 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain | 0.58 | 51.0 | 4.77e-01 | 98.8% | 93.4% |
| 3p96A02 | 3.30.70.260 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain | 0.58 | 46.0 | 4.73e-01 | 90.7% | 91.7% |
| 6k8hA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.58 | 45.0 | 3.67e-01 | 87.2% | 42.7% |
| 3fcrA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.57 | 46.0 | 3.69e-01 | 90.7% | 43.0% |
| 6g4bA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.57 | 44.0 | 3.59e-01 | 89.5% | 42.7% |
| 5i92F01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.57 | 49.0 | 3.96e-01 | 100.0% | 47.7% |
| 3lwsF02 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.57 | 46.0 | 4.33e-01 | 100.0% | 74.0% |
| 5xwkA02 | 3.30.1360.150 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › | 0.57 | 47.0 | 4.23e-01 | 94.2% | 80.2% |
| 3l44A01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.57 | 46.0 | 3.72e-01 | 100.0% | 43.7% |
| 3a8uX01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.56 | 44.0 | 3.67e-01 | 100.0% | 46.3% |
| 8dqaA01 | 3.30.429.10 | Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor | 0.56 | 44.0 | 4.32e-01 | 89.5% | 89.8% |
| 2ahoB03 | 3.30.70.1130 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha | 0.56 | 43.0 | 4.27e-01 | 83.7% | 87.5% |
| 2epjA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.55 | 46.0 | 3.71e-01 | 96.5% | 46.0% |
| 3n5mB01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.54 | 43.0 | 3.52e-01 | 89.5% | 45.5% |
| 3uuwB02 | 3.30.360.10 | Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 | 0.54 | 39.0 | 3.10e-01 | 75.6% | 61.4% |
| 7l4aA01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.54 | 39.0 | 2.98e-01 | 77.9% | 76.3% |
| 2ykyB01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.53 | 41.0 | 3.25e-01 | 87.2% | 39.2% |
| 3ca8A01 | 1.10.3620.10 | Mainly Alpha › Orthogonal Bundle › YdcF fold › YdcF like domain | 0.51 | 38.0 | 3.66e-01 | 82.6% | 95.3% |
| 2cy8A01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.51 | 44.0 | 3.47e-01 | 98.8% | 45.5% |
| 8bddA02 | 2.70.98.70 | Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › | 0.50 | 43.0 | 2.94e-01 | 100.0% | 94.7% |
| 4w91B01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.50 | 44.0 | 3.79e-01 | 100.0% | 61.6% |
ECOD (42)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3301776 | 309.1.2.1 ↗ | a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD | 0.73 | 66.0 | 5.41e-01 | 97.7% | 97.3% |
| 3622098 | 304.102.1.3 ↗ | a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_1 | 0.72 | 63.0 | 4.38e-01 | 96.5% | 91.9% |
| 3943893 | 304.28.1.2 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG | 0.72 | 55.0 | 5.41e-01 | 86.0% | 74.7% |
| 3797826 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.72 | 64.0 | 5.26e-01 | 98.8% | 69.0% |
| 3357746 | 304.12.1.8 ↗ | a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › bHLH-TF_ACT-like_plant | 0.70 | 48.0 | 5.28e-01 | 70.9% | 87.1% |
| 4005437 | 304.3.1.17 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › Sec_GG | 0.70 | 54.0 | 5.36e-01 | 87.2% | 78.9% |
| 3165390 | 304.24.1.36 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › SPOR | 0.66 | 45.0 | 4.65e-01 | 80.2% | 75.0% |
| 4416593 | 304.28.1.4 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD_1st | 0.66 | 53.0 | 5.26e-01 | 91.9% | 84.4% |
| 3947863 | 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 | 0.65 | 55.0 | 3.98e-01 | 98.8% | 32.2% |
| 3587620 | 304.55.1.22 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › MobL | 0.64 | 47.0 | 3.55e-01 | 77.9% | 40.5% |
| 3703396 | 101.1.10.0 ↗ | alpha arrays › HTH › HTH › Cyclin-like | 0.64 | 56.0 | 4.19e-01 | 100.0% | 53.3% |
| 3960051 | 327.5.1.3 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C_2 | 0.63 | 57.0 | 5.26e-01 | 100.0% | 99.1% |
| 3477384 | 327.5.1.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins | 0.63 | 57.0 | 3.62e-01 | 100.0% | 28.7% |
| 3927940 | 304.36.1.2 ↗ | a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1 | 0.63 | 55.0 | 5.20e-01 | 100.0% | 81.9% |
| 3475197 | 323.1.1.31 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-dom_DIP2-like | 0.63 | 57.0 | 3.83e-01 | 100.0% | 38.5% |
| 4975021 | 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 | 0.63 | 54.0 | 5.42e-01 | 96.5% | 98.9% |
| 5031902 | 304.24.1.5 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N | 0.63 | 42.0 | 4.55e-01 | 88.4% | 85.7% |
| 3875392 | 327.5.1.6 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-dom_DIP2-like | 0.63 | 56.0 | 4.99e-01 | 100.0% | 79.0% |
| 3800293 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.62 | 53.0 | 5.18e-01 | 95.3% | 88.2% |
| 5047888 | 304.24.1.5 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N | 0.62 | 42.0 | 4.39e-01 | 88.4% | 78.7% |
| 4970952 | 3715.1.1.1 ↗ | a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal_L22e | 0.62 | 50.0 | 5.05e-01 | 93.0% | 87.1% |
| 3955921 | 327.5.1.6 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-dom_DIP2-like | 0.62 | 55.0 | 5.05e-01 | 97.7% | 91.8% |
| 4237119 | 207.11.1.1 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD | 0.62 | 47.0 | 3.24e-01 | 83.7% | 24.0% |
| 4579088 | 327.4.1.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › YhbC-like, N-terminal domain › YhbC-like, N-terminal domain › RimP_N | 0.61 | 50.0 | 4.96e-01 | 90.7% | 97.8% |
| 5075233 | 304.24.1.5 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N | 0.61 | 42.0 | 4.39e-01 | 87.2% | 82.7% |
| 3591567 | 304.55.2.0 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like | 0.60 | 44.0 | 4.36e-01 | 77.9% | 73.3% |
| 4995957 | 310.3.1.0 ↗ | a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related | 0.60 | 46.0 | 4.96e-01 | 81.4% | 100.0% |
| 3727831 | 3012.1.1.1 ↗ | a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Trehalose_PPase | 0.59 | 49.0 | 4.92e-01 | 97.7% | 92.9% |
| 4995927 | 3715.1.1.0 ↗ | a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e | 0.59 | 47.0 | 4.71e-01 | 93.0% | 85.6% |
| 4194365 | 7577.1.1.0 ↗ | a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases | 0.58 | 42.0 | 2.51e-01 | 97.7% | 9.0% |
| 4092984 | 207.11.1.1 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD | 0.57 | 38.0 | 2.81e-01 | 74.4% | 23.1% |
| 3962316 | 873.1.1.0 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain | 0.57 | 43.0 | 3.85e-01 | 79.1% | 65.0% |
| 3596282 | 304.9.1.0 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD | 0.57 | 46.0 | 4.48e-01 | 87.2% | 88.4% |
| 4933530 | 304.24.1.5 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N | 0.56 | 37.0 | 3.92e-01 | 88.4% | 77.3% |
| 4549024 | 3016.1.1.0 ↗ | a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases | 0.56 | 45.0 | 4.18e-01 | 88.4% | 70.2% |
| 4948745 | 2006.1.1.3 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Trehalose_PPase | 0.55 | 47.0 | 3.46e-01 | 100.0% | 44.2% |
| 4168340 | 3016.1.1.0 ↗ | a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases | 0.55 | 45.0 | 4.16e-01 | 100.0% | 69.6% |
| 3738178 | 3012.1.1.0 ↗ | a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain | 0.54 | 43.0 | 4.53e-01 | 100.0% | 100.0% |
| 3603654 | 1056.1.1.1 ↗ | a+b two layers › tRNA pseudouridine synthase TruD insertion domain › tRNA pseudouridine synthase TruD insertion domain › tRNA pseudouridine synthase TruD insertion domain › TruD | 0.52 | 41.0 | 3.13e-01 | 87.2% | 51.4% |
| 4978945 | 1036.1.1.1 ↗ | a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 | 0.51 | 44.0 | 4.15e-01 | 98.8% | 77.3% |
| 3655146 | 221.1.2.0 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Alpha-L RNA-binding motif | 0.51 | 41.0 | 4.03e-01 | 90.7% | 100.0% |
| 5022358 | 242.1.1.7 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 | 0.50 | 38.0 | 3.52e-01 | 82.6% | 64.3% |
D3
medium
residues 112-133_257-276_323-381