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RdRp
Euk-VirCordyline_virus_1
RdRp__YP_009506344__Cordyline_virus_1__937809
Identity
- Accession:
- YP_009506344 ↗
- Protein ID:
- RdRp
- Kingdom:
- euk
Quality
85.4
mean pLDDT
Taxonomy
Orthornavirae›
Kitrinoviricota›
Alsuviricetes›
Martellivirales›
Closteroviridae›
Velarivirus›
Cordyline_virus_1
TaxID: 937809
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 45-50_427-518
Domain cluster:
rep: RNA-dependent_RNA_polymerase,_partial__YP_009241367__Grapevine_leafroll-associated_virus_13__1815581__D413-491
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 42.8 | 4.70e-11 | 91.8% | 18.4% |
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3ck6C02 | 1.20.58.340 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region | 0.60 | 49.0 | 4.61e-01 | 87.8% | 79.8% |
| 1wkbA03 | 1.10.730.10 | Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 | 0.55 | 41.0 | 3.84e-01 | 90.8% | 63.6% |
| 4h9nC00 | 1.20.58.2170 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.54 | 35.0 | 2.82e-01 | 90.8% | 31.7% |
| 1sumB01 | 1.20.58.220 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 | 0.54 | 44.0 | 4.31e-01 | 89.8% | 85.0% |
| 2vwaA00 | 1.20.58.1330 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Plasmodium falciparum UIS3 membrane protein | 0.53 | 39.0 | 3.92e-01 | 89.8% | 75.8% |
| 2nwbA02 | 1.20.58.480 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.53 | 42.0 | 3.19e-01 | 84.7% | 78.1% |
| 1ug7A00 | 1.20.120.360 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Axin interactor, dorsalization-associated protein, N-terminal domain | 0.52 | 43.0 | 4.04e-01 | 93.9% | 72.7% |
| 1e3mB04 | 1.10.1420.10 | Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › | 0.51 | 41.0 | 3.65e-01 | 90.8% | 80.3% |
| 6zxqA01 | 1.10.300.10 | Mainly Alpha › Orthogonal Bundle › Adenylosuccinate Synthetase, subunit A; domain 2 › Adenylosuccinate Synthetase, subunit A, domain 2 | 0.51 | 41.0 | 4.22e-01 | 99.0% | 92.5% |
| 4x28C03 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.50 | 40.0 | 3.56e-01 | 86.7% | 75.5% |
ECOD (15)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3504301 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.62 | 49.0 | 4.74e-01 | 84.7% | 86.4% |
| 4997991 | 7516.1.1.2 ↗ | a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 | 0.61 | 49.0 | 3.41e-01 | 87.8% | 57.6% |
| 3519581 | 604.12.1.4 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 | 0.59 | 46.0 | 4.17e-01 | 83.7% | 77.8% |
| 3616669 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.58 | 47.0 | 4.49e-01 | 87.8% | 90.4% |
| 3188597 | 604.12.1.0 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain | 0.57 | 44.0 | 4.55e-01 | 86.7% | 90.0% |
| 3484930 | 604.1.1.1 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin | 0.57 | 45.0 | 4.41e-01 | 84.7% | 86.7% |
| 4030256 | 603.2.1.0 ↗ | alpha bundles › STAT-like › STAT › STAT | 0.56 | 41.0 | 4.15e-01 | 84.7% | 80.0% |
| 3178149 | 604.1.1.96 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Bap31 | 0.55 | 44.0 | 4.24e-01 | 88.8% | 84.3% |
| 54312 | 633.16.1.0 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like | 0.54 | 38.0 | 3.89e-01 | 87.8% | 75.3% |
| 3170802 | 101.1.1.133 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › Vhr1 | 0.54 | 41.0 | 4.18e-01 | 89.8% | 83.2% |
| 3618144 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.52 | 40.0 | 2.90e-01 | 84.7% | 53.4% |
| 3516129 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.52 | 41.0 | 4.08e-01 | 87.8% | 97.1% |
| 3628698 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.52 | 42.0 | 3.99e-01 | 87.8% | 88.7% |
| 3480768 | 101.1.1.286 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › PF27813 | 0.51 | 35.0 | 3.51e-01 | 95.9% | 66.7% |
| 3383904 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.50 | 34.0 | 2.96e-01 | 78.6% | 43.2% |
D2
high
residues 59-121
Domain cluster:
rep: ORF1b__YP_001816770__Bean_yellow_disorder_virus__267970__D77-131
D3
high
residues 132-259_292-366
Domain cluster:
rep: ORF1b__YP_001816770__Bean_yellow_disorder_virus__267970__D132-368
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 94.8 | 8.10e-27 | 63.5% | 28.4% |
| PF00978.27 | RdRP_2 | 50.2 | 2.70e-13 | 37.0% | 17.3% |
D4
medium
residues 260-291_367-426
Domain cluster:
rep: RNA_dependent_RNA_polymerase,_partial__YP_002364303__Grapevine_leafroll-associated_virus_10__367121__D252-284_355-434
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 60.9 | 1.50e-16 | 66.3% | 13.2% |
CATH (21)
| 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 | 0.76 | 70.0 | 6.00e-01 | 100.0% | 92.2% |
| 5wm1A02 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.72 | 49.0 | 4.67e-01 | 70.7% | 87.2% |
| 5cqgA04 | 3.30.70.2630 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.68 | 60.0 | 5.75e-01 | 96.7% | 92.5% |
| 3mtkA00 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.67 | 54.0 | 4.49e-01 | 87.0% | 82.8% |
| 3h5xA03 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.66 | 54.0 | 5.05e-01 | 89.1% | 96.6% |
| 1x4hA00 | 3.30.70.330 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain | 0.64 | 45.0 | 4.20e-01 | 71.7% | 81.1% |
| 3dkxA01 | 3.40.1310.30 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.63 | 44.0 | 3.94e-01 | 73.9% | 96.3% |
| 6h8oA00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.57 | 42.0 | 4.16e-01 | 77.2% | 96.8% |
| 2f06A00 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.56 | 42.0 | 3.63e-01 | 79.3% | 91.7% |
| 6foqA03 | 3.40.462.20 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › | 0.56 | 43.0 | 3.37e-01 | 84.8% | 54.8% |
| 3cjsA00 | 3.30.70.1170 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sun protein; domain 3 | 0.56 | 35.0 | 4.18e-01 | 78.3% | 100.0% |
| 3znuA00 | 3.30.70.1060 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel | 0.55 | 40.0 | 4.05e-01 | 77.2% | 98.9% |
| 1h3dA03 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.55 | 38.0 | 4.38e-01 | 76.1% | 100.0% |
| 4p0dA02 | 2.60.40.740 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.54 | 39.0 | 3.25e-01 | 76.1% | 70.0% |
| 1ayeA01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.54 | 41.0 | 4.09e-01 | 82.6% | 88.9% |
| 1lfpA03 | 3.30.70.980 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain | 0.54 | 40.0 | 4.45e-01 | 88.0% | 100.0% |
| 1jqgA01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.53 | 41.0 | 4.13e-01 | 82.6% | 93.4% |
| 1mw7A03 | 3.30.70.980 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain | 0.53 | 38.0 | 4.11e-01 | 76.1% | 100.0% |
| 3bv8A00 | 3.30.70.250 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding | 0.51 | 38.0 | 3.97e-01 | 81.5% | 89.4% |
| 3d68A01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.51 | 38.0 | 3.89e-01 | 81.5% | 95.7% |
| 3n28A02 | 3.30.70.2020 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.51 | 44.0 | 4.25e-01 | 98.9% | 96.2% |
ECOD (27)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4950570 | 304.163.1.0 ↗ | a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain | 0.65 | 45.0 | 5.14e-01 | 76.1% | 100.0% |
| 5036777 | 304.3.1.0 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain | 0.63 | 46.0 | 4.97e-01 | 76.1% | 98.7% |
| 3194712 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.60 | 47.0 | 3.32e-01 | 84.8% | 41.1% |
| 5071792 | 304.3.1.0 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain | 0.58 | 41.0 | 4.50e-01 | 75.0% | 97.3% |
| 1711536 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.57 | 43.0 | 3.21e-01 | 81.5% | 47.4% |
| 4461494 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.57 | 39.0 | 4.50e-01 | 75.0% | 100.0% |
| 3164278 | 304.8.1.25 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF5609 | 0.57 | 40.0 | 4.07e-01 | 72.8% | 88.9% |
| 3394715 | 304.7.1.1 ↗ | a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 | 0.56 | 43.0 | 4.49e-01 | 83.7% | 97.6% |
| 4058379 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.55 | 38.0 | 4.40e-01 | 71.7% | 100.0% |
| 5026454 | 304.126.1.0 ↗ | a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C | 0.55 | 38.0 | 4.29e-01 | 82.6% | 100.0% |
| 4502075 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.55 | 39.0 | 4.41e-01 | 80.4% | 100.0% |
| 4215974 | 304.22.1.1 ↗ | a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C | 0.54 | 39.0 | 4.37e-01 | 81.5% | 98.6% |
| 4319410 | 304.15.1.7 ↗ | a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain › DUF5609 | 0.54 | 38.0 | 3.93e-01 | 72.8% | 90.6% |
| 2698983 | 304.11.1.1 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Acyl_transf_1 | 0.54 | 39.0 | 4.19e-01 | 76.1% | 87.7% |
| 5016775 | 304.122.1.1 ↗ | a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 | 0.54 | 42.0 | 4.04e-01 | 83.7% | 76.2% |
| 4212820 | 2006.1.1.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like | 0.54 | 39.0 | 2.83e-01 | 79.3% | 97.0% |
| 4949196 | 304.117.1.0 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC | 0.53 | 34.0 | 4.00e-01 | 75.0% | 100.0% |
| 4507546 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.53 | 38.0 | 4.32e-01 | 79.3% | 100.0% |
| 3516259 | 304.8.1.25 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF5609 | 0.53 | 38.0 | 3.72e-01 | 77.2% | 84.8% |
| 4954773 | 304.4.1.0 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel | 0.52 | 40.0 | 3.76e-01 | 82.6% | 67.0% |
| 4986600 | 304.8.1.12 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_8 | 0.52 | 38.0 | 3.57e-01 | 79.3% | 83.3% |
| 5062189 | 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 | 0.52 | 39.0 | 4.20e-01 | 82.6% | 97.3% |
| 3998804 | 304.9.1.0 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD | 0.52 | 35.0 | 3.73e-01 | 73.9% | 81.2% |
| 4156338 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.51 | 38.0 | 4.13e-01 | 81.5% | 98.7% |
| 5000640 | 304.24.1.0 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like | 0.51 | 35.0 | 4.04e-01 | 77.2% | 100.0% |
| 3253994 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.51 | 37.0 | 2.68e-01 | 79.3% | 41.9% |
| 4570602 | 304.24.1.0 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like | 0.50 | 35.0 | 3.85e-01 | 72.8% | 100.0% |