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RNA-dependent_RNA_polymerase
Euk-VirPenicillium_chrysogenum_virus
RNA-dependent_RNA_polymerase__YP_392482__Penicillium_chrysogenum_virus__158372
Identity
- Accession:
- YP_392482 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
77.0
mean pLDDT
Taxonomy
Orthornavirae›
Duplornaviricota›
Chrymotiviricetes›
Ghabrivirales›
Chrysoviridae›
Alphachrysovirus›
Penicillium_chrysogenum_virus
TaxID: 158372
Cluster
View cluster (8 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 326-456_828-856
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009667008__Macrophomina_phaseolina_chrysovirus_1__1708483__D328-448
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 35.6 | 7.80e-09 | 80.6% | 23.9% |
D2
medium
residues 71-235
Domain cluster:
rep: VP2__YP_009665170__Eriocheir_sinensis_reovirus__273810__D721-872
D3
medium
residues 236-325
D4
medium
residues 512-635_671-730
D5
medium
residues 636-670_731-826
Domain cluster:
rep: RNA-directed_RNA-polymerase__YP_009667012__Colletotrichum_gloeosporioides_chrysovirus_1__1766766__D621-641_716-788
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 99.4 | 3.40e-28 | 74.1% | 19.6% |
D6
medium
residues 857-930_969-1001
Domain cluster:
representative
D7
medium
residues 931-968_1014-1060
Domain cluster:
representative
CATH (3)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3dv9A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.55 | 34.0 | 3.64e-01 | 85.9% | 72.9% |
| 1gq2A02 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.53 | 39.0 | 2.68e-01 | 78.8% | 78.0% |
| 4s3mB02 | 1.10.1040.10 | Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 | 0.53 | 46.0 | 4.30e-01 | 96.5% | 100.0% |
D8
medium
residues 1002-1013_1061-1117
Domain cluster:
representative
CATH (35)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4m70B00 | 1.10.246.200 | Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain | 0.77 | 58.0 | 5.28e-01 | 79.7% | 92.3% |
| 5ci5B02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.76 | 54.0 | 3.81e-01 | 75.4% | 76.0% |
| 2xd3A02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.73 | 52.0 | 3.70e-01 | 73.9% | 76.3% |
| 3if8B02 | 1.20.58.730 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.73 | 51.0 | 4.56e-01 | 73.9% | 69.0% |
| 3uorB02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.73 | 57.0 | 4.02e-01 | 84.1% | 75.2% |
| 1j5sA01 | 3.20.20.140 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases | 0.72 | 53.0 | 3.33e-01 | 78.3% | 96.7% |
| 3qufA02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.71 | 50.0 | 3.44e-01 | 73.9% | 78.6% |
| 4ovjA02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.71 | 52.0 | 3.65e-01 | 78.3% | 77.7% |
| 4jd9G00 | 1.10.238.20 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain | 0.70 | 55.0 | 4.50e-01 | 82.6% | 62.5% |
| 1eu8A02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.70 | 52.0 | 3.68e-01 | 79.7% | 76.0% |
| 4rjzA02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.67 | 52.0 | 3.76e-01 | 84.1% | 74.5% |
| 1rp3G02 | 1.20.140.160 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › PhyR, sigma-like (SL) domain | 0.66 | 49.0 | 3.88e-01 | 79.7% | 66.9% |
| 4e69A00 | 3.40.1190.20 | Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase | 0.66 | 52.0 | 3.43e-01 | 88.4% | 82.6% |
| 2ougA00 | 3.30.70.940 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain | 0.65 | 48.0 | 3.80e-01 | 79.7% | 66.0% |
| 4ex8A00 | 3.40.1790.10 | Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain | 0.64 | 48.0 | 3.18e-01 | 82.6% | 49.8% |
| 3hx3A01 | 1.10.8.20 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p | 0.63 | 44.0 | 4.49e-01 | 73.9% | 88.1% |
| 1txuA01 | 1.10.246.120 | Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › | 0.62 | 55.0 | 4.95e-01 | 98.6% | 88.3% |
| 3u61D03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.61 | 46.0 | 4.28e-01 | 82.6% | 63.7% |
| 4hiaA00 | 3.30.450.20 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain | 0.61 | 52.0 | 3.89e-01 | 95.7% | 59.7% |
| 3c18A02 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.61 | 46.0 | 3.88e-01 | 81.2% | 66.1% |
| 6xzqA01 | 3.40.91.90 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain | 0.61 | 47.0 | 3.58e-01 | 82.6% | 91.4% |
| 1rykA00 | 1.10.1470.10 | Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › YjbJ | 0.60 | 42.0 | 4.28e-01 | 91.3% | 75.4% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.59 | 44.0 | 4.52e-01 | 95.7% | 82.1% |
| 2i53A02 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.59 | 44.0 | 3.86e-01 | 82.6% | 58.6% |
| 2pmrA00 | 1.20.1270.90 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like | 0.58 | 43.0 | 4.21e-01 | 78.3% | 90.8% |
| 2mh3A00 | 4.10.280.10 | Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Helix-loop-helix DNA-binding domain | 0.58 | 37.0 | 3.73e-01 | 76.8% | 64.3% |
| 3vayA02 | 1.20.120.1600 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.58 | 50.0 | 4.64e-01 | 95.7% | 85.1% |
| 2oo2A00 | 1.20.1270.90 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like | 0.58 | 44.0 | 4.26e-01 | 81.2% | 82.9% |
| 3t46A00 | 1.20.1270.10 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.57 | 41.0 | 4.03e-01 | 76.8% | 77.3% |
| 4didB01 | 1.20.58.450 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cell division control protein 42 homolog | 0.56 | 45.0 | 3.90e-01 | 91.3% | 69.3% |
| 2yi9A05 | 1.20.1270.270 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › VP1, C-terminal extension domain | 0.56 | 41.0 | 3.99e-01 | 79.7% | 71.4% |
| 4ap9A02 | 1.10.150.210 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Phosphoserine phosphatase; domain 2 | 0.55 | 35.0 | 3.77e-01 | 81.2% | 75.0% |
| 8e9gK01 | 1.10.287.3510 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.54 | 41.0 | 3.80e-01 | 84.1% | 76.9% |
| 2el7A02 | 1.10.240.10 | Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase | 0.53 | 40.0 | 3.60e-01 | 82.6% | 58.5% |
| 6zhiB02 | 1.20.1270.10 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.51 | 38.0 | 3.65e-01 | 82.6% | 79.5% |
ECOD (22)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5010827 | 7523.1.1.28 ↗ | a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_8 | 0.79 | 63.0 | 3.82e-01 | 84.1% | 60.0% |
| 4972100 | 7523.1.1.0 ↗ | a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II | 0.74 | 56.0 | 3.76e-01 | 79.7% | 73.5% |
| 5069340 | 4163.1.1.1 ↗ | alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 | 0.74 | 43.0 | 3.51e-01 | 97.1% | 33.3% |
| 4940746 | 3457.1.1.1 ↗ | alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 | 0.73 | 52.0 | 3.76e-01 | 73.9% | 40.0% |
| 4039740 | 3317.1.1.2 ↗ | alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain › HTH_ParB | 0.73 | 47.0 | 4.85e-01 | 78.3% | 70.8% |
| 3065995 | 148.1.3.0 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain | 0.71 | 54.0 | 3.92e-01 | 82.6% | 54.1% |
| 3961339 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.71 | 52.0 | 4.16e-01 | 78.3% | 91.9% |
| 321266 | 2002.1.1.98 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › UxaC | 0.71 | 55.0 | 3.31e-01 | 84.1% | 97.5% |
| 5005181 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.69 | 53.0 | 3.95e-01 | 82.6% | 90.3% |
| 3963102 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.68 | 51.0 | 4.06e-01 | 79.7% | 87.9% |
| 3968663 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.65 | 47.0 | 4.01e-01 | 76.8% | 85.2% |
| 4942062 | 632.11.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like | 0.64 | 46.0 | 4.34e-01 | 76.8% | 87.1% |
| 5027497 | 632.6.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit | 0.63 | 48.0 | 4.56e-01 | 81.2% | 97.5% |
| 4946474 | 3317.1.1.0 ↗ | alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain | 0.61 | 41.0 | 4.25e-01 | 75.4% | 73.8% |
| 4949146 | 632.11.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like | 0.61 | 46.0 | 4.32e-01 | 79.7% | 92.8% |
| 5044025 | 632.1.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain | 0.60 | 44.0 | 4.17e-01 | 78.3% | 89.4% |
| 4088578 | 101.35.1.0 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX | 0.60 | 48.0 | 4.97e-01 | 95.7% | 96.9% |
| 4942424 | 632.11.1.1 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 | 0.58 | 43.0 | 4.22e-01 | 81.2% | 86.7% |
| 3520403 | 633.6.1.6 ↗ | alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACAD9-ACADV_C | 0.57 | 42.0 | 3.66e-01 | 78.3% | 82.9% |
| 3435434 | 632.1.1.13 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Rx_N | 0.57 | 43.0 | 3.72e-01 | 79.7% | 83.8% |
| 3810451 | 632.1.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain | 0.52 | 39.0 | 3.65e-01 | 81.2% | 84.4% |
| 5070372 | 164.1.1.0 ↗ | alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II | 0.51 | 42.0 | 3.90e-01 | 95.7% | 78.9% |