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RNA-dependent_RNA_polymerase
Euk-VirBeihai_narna-like_virus_18
RNA-dependent_RNA_polymerase__YP_009333315__Beihai_narna-like_virus_18__1922445
Identity
- Accession:
- YP_009333315 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
72.4
mean pLDDT
Cluster
View cluster (11 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 22-107
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009333153__Beihai_narna-like_virus_14__1922441__D1-76
CATH (12)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3ay5A01 | 1.20.1420.10 | Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain | 0.61 | 47.0 | 4.09e-01 | 82.6% | 91.7% |
| 1zmbA02 | 6.10.170.10 | Special › Helix non-globular › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › | 0.60 | 28.0 | 3.88e-01 | 93.0% | 100.0% |
| 3r84B00 | 6.10.280.160 | Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 | 0.58 | 39.0 | 4.09e-01 | 81.4% | 75.0% |
| 4n6cB00 | 1.20.120.450 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain | 0.55 | 49.0 | 3.87e-01 | 98.8% | 70.7% |
| 5jc3A02 | 1.20.1320.30 | Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › | 0.53 | 37.0 | 3.29e-01 | 72.1% | 96.0% |
| 4l8jA04 | 1.10.287.470 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin | 0.53 | 34.0 | 3.93e-01 | 80.2% | 98.3% |
| 7ckaA01 | 1.20.910.10 | Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like | 0.52 | 45.0 | 3.50e-01 | 98.8% | 57.4% |
| 3hcwA01 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.52 | 36.0 | 3.13e-01 | 72.1% | 92.9% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.52 | 30.0 | 3.30e-01 | 98.8% | 70.1% |
| 3fayA00 | 1.10.506.10 | Mainly Alpha › Orthogonal Bundle › GTPase Activation - p120GAP; domain 1 › GTPase Activation - p120gap; domain 1 | 0.52 | 44.0 | 2.90e-01 | 96.5% | 51.2% |
| 2fzlA02 | 6.10.140.1180 | Special › Helix non-globular › Helix Hairpins › | 0.50 | 33.0 | 3.77e-01 | 81.4% | 93.5% |
| 1fs0G02 | 1.10.287.80 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain | 0.50 | 38.0 | 3.79e-01 | 81.4% | 79.8% |
ECOD (6)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2168246 | 1176.1.1.1 ↗ | alpha arrays › Nitrogenase vanadium-iron protein delta chain › Nitrogenase vanadium-iron protein delta chain › Nitrogenase vanadium-iron protein delta chain › AnfG_VnfG | 0.65 | 58.0 | 5.35e-01 | 100.0% | 86.7% |
| 4347845 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.62 | 54.0 | 3.94e-01 | 98.8% | 68.0% |
| 3970787 | 2002.1.1.0 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels | 0.54 | 48.0 | 3.33e-01 | 100.0% | 96.0% |
| 3227022 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.53 | 33.0 | 3.38e-01 | 98.8% | 62.4% |
| 4034208 | 1075.3.1.4 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC importer transmembrane domain fold › Type I ABC importer transmembrane domain fold › BPD_transp_1+BPD_transp_1_N | 0.51 | 44.0 | 3.09e-01 | 100.0% | 65.6% |
| 3411883 | 604.1.1.63 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_SESTD1 | 0.51 | 45.0 | 3.97e-01 | 95.3% | 83.3% |
D2
high
residues 208-359_391-427
Domain cluster:
rep: replication_associated_protein__YP_009345107__Amphibola_crenata_associated_bacilladnavirus_1__1941435__D302-478
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00910.29 best | RNA_helicase | 98.1 | 5.60e-28 | 56.6% | 98.1% |
D3
medium
residues 108-188_583-627
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009333153__Beihai_narna-like_virus_14__1922441__D77-145_426-451_481-543
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6juvB01 | 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 | 0.55 | 20.0 | 2.51e-01 | 97.6% | 52.0% |
D4
medium
residues 429-494
Domain cluster:
representative
CATH (3)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3gqqA00 | 2.70.50.40 | Mainly Beta › Distorted Sandwich › Coagulation Factor XIII; Chain A, domain 1 › GMP phosphodiesterase, delta subunit | 0.56 | 38.0 | 2.83e-01 | 71.2% | 34.7% |
| 4hscX04 | 2.60.40.1430 | Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 | 0.54 | 38.0 | 3.31e-01 | 75.8% | 85.5% |
| 4ivkA00 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.51 | 35.0 | 2.28e-01 | 75.8% | 30.4% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3482279 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.60 | 43.0 | 3.14e-01 | 77.3% | 42.5% |
| 2142463 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.60 | 43.0 | 2.62e-01 | 80.3% | 70.6% |
| 4968312 | 2484.1.1.66 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_3 | 0.54 | 42.0 | 3.03e-01 | 89.4% | 85.5% |
| 3898917 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.53 | 36.0 | 2.95e-01 | 72.7% | 81.4% |
| 3250040 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.53 | 36.0 | 3.03e-01 | 72.7% | 75.2% |
| 3711130 | 11.1.5.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f | 0.52 | 37.0 | 2.80e-01 | 77.3% | 40.5% |
| 4065437 | 11.13.1.1 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Leukocidin-like › Leukocidin-like › Leukocidin | 0.52 | 41.0 | 2.72e-01 | 87.9% | 58.3% |
| 3694008 | 6.1.1.10 ↗ | beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › FRG1 | 0.51 | 39.0 | 2.92e-01 | 84.8% | 96.8% |
D5
medium
residues 495-582_628-720
D6
medium
residues 798-933
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009333164__Beihai_narna-like_virus_19__1922446__D873-1053
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3f1iS00 | 1.20.5.1940 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.75 | 19.0 | 2.66e-01 | 89.7% | 42.9% |
| 4fmrA02 | 4.10.520.10 | Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins | 0.67 | 23.0 | 2.82e-01 | 97.8% | 46.6% |
| 1ah5A03 | 3.30.160.40 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain | 0.63 | 30.0 | 3.63e-01 | 97.1% | 68.6% |
| 2d3o100 | 3.30.70.1050 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain | 0.56 | 26.0 | 3.00e-01 | 97.8% | 59.0% |
| 2zdiB00 | 1.10.287.370 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.55 | 27.0 | 3.06e-01 | 100.0% | 59.4% |
| 2kx2A00 | 3.30.780.30 | Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › | 0.50 | 29.0 | 3.36e-01 | 87.5% | 79.2% |
ECOD (28)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4638787 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.74 | 33.0 | 4.28e-01 | 96.3% | 72.5% |
| 4040973 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.70 | 31.0 | 4.17e-01 | 94.9% | 78.6% |
| 4558929 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.68 | 32.0 | 4.05e-01 | 98.5% | 75.0% |
| 4187672 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.66 | 31.0 | 4.06e-01 | 97.8% | 78.7% |
| 4359254 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.66 | 28.0 | 3.67e-01 | 93.4% | 69.3% |
| 4087213 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.66 | 29.0 | 3.74e-01 | 94.1% | 72.0% |
| 4460237 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.63 | 28.0 | 3.58e-01 | 94.1% | 70.7% |
| 4132764 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.62 | 30.0 | 3.67e-01 | 97.8% | 70.6% |
| 4175367 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.62 | 31.0 | 3.66e-01 | 97.8% | 68.9% |
| 4638542 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.61 | 30.0 | 3.52e-01 | 97.8% | 64.2% |
| 4975692 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.61 | 30.0 | 3.57e-01 | 97.8% | 67.8% |
| 4025655 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.58 | 26.0 | 3.10e-01 | 100.0% | 58.9% |
| 4646686 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.58 | 27.0 | 3.69e-01 | 93.4% | 85.7% |
| 3839010 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.58 | 30.0 | 3.74e-01 | 97.1% | 80.0% |
| 3282536 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.58 | 30.0 | 3.76e-01 | 97.1% | 83.7% |
| 3394225 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.57 | 26.0 | 2.80e-01 | 100.0% | 48.7% |
| 4434012 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.57 | 31.0 | 3.76e-01 | 96.3% | 82.4% |
| 3267746 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.57 | 29.0 | 3.56e-01 | 97.8% | 76.5% |
| 3630462 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.57 | 28.0 | 2.86e-01 | 100.0% | 46.4% |
| 3538408 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.56 | 26.0 | 3.08e-01 | 100.0% | 61.1% |
| 4965501 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.56 | 29.0 | 3.42e-01 | 97.1% | 72.2% |
| 3229643 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.56 | 27.0 | 2.94e-01 | 100.0% | 52.5% |
| 3783976 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.56 | 28.0 | 3.42e-01 | 100.0% | 73.3% |
| 4973433 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.55 | 29.0 | 3.42e-01 | 97.1% | 74.4% |
| 3228583 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.55 | 27.0 | 2.95e-01 | 100.0% | 54.8% |
| 3373588 | 3887.2.1.1 ↗ | a+b two layers › Yeast killer toxin-like › Antifungal protein ginkbilobin-2 › Antifungal protein ginkbilobin-2 › Stress-antifung | 0.54 | 26.0 | 2.80e-01 | 97.1% | 50.0% |
| 3254236 | 192.2.1.0 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin | 0.54 | 29.0 | 3.23e-01 | 100.0% | 65.7% |
| 3718200 | 192.2.1.0 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin | 0.51 | 25.0 | 2.62e-01 | 100.0% | 48.8% |