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RNA-dependent_RNA_polymerase
Euk-VirXanthophyllomyces_dendrorhous_virus_L1A
RNA-dependent_RNA_polymerase__YP_007697651__Xanthophyllomyces_dendrorhous_virus_L1A__1167690
Identity
- Accession:
- YP_007697651 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
87.4
mean pLDDT
Cluster
View cluster (56 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 75-210_538-559
D2
medium
residues 233-278_401-440
Domain cluster:
rep: hypothetical_protein_2__YP_009342434__Wuhan_insect_virus_27__1923731__D275-301_438-483
CATH (11)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2fu2A00 | 1.20.1440.50 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like | 0.71 | 33.0 | 3.53e-01 | 91.9% | 50.0% |
| 2vugA04 | 1.20.58.2250 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 32.0 | 3.19e-01 | 96.5% | 48.9% |
| 2zxqA06 | 1.20.1270.70 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle | 0.57 | 30.0 | 3.36e-01 | 93.0% | 65.2% |
| 4p9fA01 | 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 | 0.56 | 39.0 | 4.37e-01 | 81.4% | 92.5% |
| 2rkkA01 | 1.25.40.270 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 | 0.55 | 50.0 | 4.05e-01 | 98.8% | 98.7% |
| 6guvA00 | 3.30.710.10 | Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A | 0.53 | 34.0 | 2.93e-01 | 81.4% | 41.8% |
| 1z21A00 | 1.10.10.1000 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Type III secretion system virulence factor YopR, core domain | 0.52 | 43.0 | 4.20e-01 | 91.9% | 86.5% |
| 2ig3A00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.51 | 41.0 | 3.59e-01 | 86.0% | 78.0% |
| 3dynA00 | 1.10.1300.10 | Mainly Alpha › Orthogonal Bundle › Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b › 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain | 0.51 | 40.0 | 2.84e-01 | 91.9% | 83.5% |
| 3lewA01 | 1.25.40.390 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.50 | 43.0 | 2.99e-01 | 98.8% | 65.5% |
| 3hl6A02 | 1.20.58.700 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.50 | 41.0 | 3.74e-01 | 90.7% | 80.0% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4856112 | 131.1.1.15 ↗ | alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Ppx-GppA_III | 0.57 | 31.0 | 3.20e-01 | 97.7% | 53.7% |
| 3580700 | 148.1.3.10 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_6 | 0.55 | 31.0 | 2.91e-01 | 95.3% | 44.8% |
| 3481387 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.54 | 47.0 | 4.22e-01 | 96.5% | 87.5% |
| 4021091 | 150.5.1.84 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › Cation_efflux | 0.54 | 43.0 | 3.51e-01 | 88.4% | 90.6% |
| 4989912 | 131.1.1.0 ↗ | alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like | 0.53 | 41.0 | 3.15e-01 | 86.0% | 73.6% |
| 2755249 | 148.1.3.10 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_6 | 0.53 | 30.0 | 2.86e-01 | 95.3% | 46.0% |
| 4025482 | 3407.1.1.1 ↗ | mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › NOP5NT | 0.52 | 38.0 | 3.18e-01 | 76.7% | 76.8% |
| 4992205 | 129.1.1.16 ↗ | alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 | 0.52 | 38.0 | 3.50e-01 | 79.1% | 90.4% |
D3
medium
residues 356-400_455-537
Domain cluster:
rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 24.4 | 1.60e-05 | 84.4% | 18.0% |
| PF02123.22 | RdRP_4 | 60.6 | 2.00e-16 | 66.4% | 17.6% |
D4
medium
residues 560-695
Domain cluster:
rep: putative_RNA-dependent_RNA_polymerase__YP_009225665__Panax_notoginseng_virus_A__1777016__D641-759
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4ixjA01 | 3.30.1300.80 | Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › | 0.53 | 28.0 | 3.57e-01 | 98.5% | 89.6% |
| 2damA00 | 1.10.8.10 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain | 0.51 | 22.0 | 3.04e-01 | 73.5% | 79.1% |
D5
medium
residues 696-761
Domain cluster:
rep: RNA_dependent_RNA_polymerase__YP_009182181__Red_clover_powdery_mildew-associated_totivirus_3__1714364__D745-799
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3iqtA01 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.60 | 41.0 | 3.52e-01 | 72.7% | 79.8% |
| 7craA02 | 1.20.58.1480 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.55 | 38.0 | 3.51e-01 | 74.2% | 68.5% |