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RNA-dependent_RNA_polymerase
Euk-VirBeihai_weivirus-like_virus_5
RNA-dependent_RNA_polymerase__YP_009337004__Beihai_weivirus-like_virus_5__1922753
Identity
- Accession:
- YP_009337004 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
82.5
mean pLDDT
Cluster
View cluster (18 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 13-181
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009337047__Beihai_weivirus-like_virus_7__1922754__D6-140
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6r1nA01 | 1.10.287.40 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain | 0.60 | 36.0 | 4.46e-01 | 71.6% | 98.1% |
| 6vudA01 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.60 | 33.0 | 4.04e-01 | 86.4% | 83.5% |
| 3lssA01 | 1.10.287.40 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain | 0.59 | 38.0 | 4.47e-01 | 88.2% | 95.5% |
| 2wdqD00 | 1.20.1300.10 | Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit | 0.59 | 30.0 | 3.66e-01 | 81.7% | 76.2% |
| 2i0mA01 | 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 | 0.57 | 29.0 | 3.55e-01 | 81.7% | 75.5% |
| 4egwA02 | 1.20.58.340 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region | 0.55 | 32.0 | 3.73e-01 | 82.8% | 80.7% |
| 1oahA02 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.52 | 31.0 | 3.35e-01 | 88.2% | 67.6% |
| 3r6nA02 | 1.20.58.1060 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.52 | 32.0 | 3.37e-01 | 97.6% | 65.8% |
| 2yn7A00 | 1.10.3160.10 | Mainly Alpha › Orthogonal Bundle › Bbcrasp-1 › Bbcrasp-1 | 0.51 | 36.0 | 3.35e-01 | 72.2% | 64.0% |
| 5xdcB01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.50 | 27.0 | 3.17e-01 | 92.3% | 74.8% |
ECOD (9)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3389713 | 174.1.1.29 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF4728 | 0.59 | 31.0 | 3.44e-01 | 83.4% | 60.0% |
| 3579266 | 5055.1.1.11 ↗ | extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel › Cation_ATPase_N | 0.58 | 28.0 | 3.94e-01 | 72.2% | 100.0% |
| 3578256 | 5055.1.1.0 ↗ | extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel | 0.57 | 26.0 | 3.81e-01 | 88.8% | 100.0% |
| 3581772 | 4177.1.1.8 ↗ | alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 | 0.57 | 40.0 | 3.37e-01 | 70.4% | 58.2% |
| 4977678 | 192.1.1.50 ↗ | alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › EMC3_TMCO1 | 0.55 | 31.0 | 3.23e-01 | 74.6% | 57.5% |
| 3250802 | 611.2.1.0 ↗ | alpha bundles › N-cbl like › N-terminal domain of cbl (N-cbl) › N-terminal domain of cbl (N-cbl) | 0.53 | 33.0 | 3.32e-01 | 71.6% | 60.6% |
| 3191139 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.52 | 37.0 | 3.66e-01 | 71.6% | 94.9% |
| 4944191 | 3755.3.1.0 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin | 0.52 | 37.0 | 4.08e-01 | 74.6% | 90.6% |
| 3459613 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.50 | 36.0 | 3.64e-01 | 72.2% | 91.5% |
D2
medium
residues 264-313
Domain cluster:
representative
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3pp2A00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.63 | 48.0 | 3.86e-01 | 88.0% | 82.1% |
| 2giaA00 | 2.30.31.40 | Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › | 0.57 | 44.0 | 3.34e-01 | 94.0% | 73.4% |
| 2k2jA00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.56 | 43.0 | 3.37e-01 | 88.0% | 74.4% |
| 2xn1A01 | 2.70.98.60 | Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › alpha-galactosidase from lactobacil brevis | 0.53 | 41.0 | 2.70e-01 | 96.0% | 58.4% |
| 2a0uB01 | 1.20.120.420 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 | 0.53 | 40.0 | 2.90e-01 | 100.0% | 26.9% |
| 4owzA00 | 3.10.130.10 | Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain | 0.52 | 40.0 | 3.19e-01 | 98.0% | 83.6% |
| 2nqwA00 | 3.30.465.10 | Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › | 0.51 | 37.0 | 3.23e-01 | 84.0% | 47.1% |
| 2i9wA00 | 3.10.450.50 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.51 | 41.0 | 3.00e-01 | 100.0% | 73.9% |
| 5jk0B01 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.51 | 37.0 | 2.71e-01 | 84.0% | 31.2% |
| 2r41A00 | 3.10.450.150 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein | 0.51 | 36.0 | 3.05e-01 | 82.0% | 38.8% |
| 4gq1A00 | 2.130.10.10 | Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase | 0.51 | 40.0 | 2.48e-01 | 92.0% | 38.6% |
| 3l4rA00 | 2.40.128.20 | Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain | 0.51 | 37.0 | 2.82e-01 | 86.0% | 69.5% |
| 2iecD00 | 3.30.1300.20 | Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 7,8-dihydroneopterin aldolase (MptD) | 0.51 | 37.0 | 3.01e-01 | 86.0% | 88.9% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3280385 | 4.8.1.5 ↗ | beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR | 0.61 | 44.0 | 4.33e-01 | 78.0% | 70.9% |
| 3686122 | 633.23.1.9 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 | 0.60 | 48.0 | 3.20e-01 | 94.0% | 29.5% |
| 4177358 | 4947.1.1.1 ↗ | a+b complex topology › barrel domain in MalF N-terminal region › barrel domain in MalF N-terminal region › barrel domain in MalF N-terminal region › MalF_P2 | 0.59 | 45.0 | 3.90e-01 | 90.0% | 55.6% |
| 3492622 | 3338.1.1.0 ↗ | a+b two layers › Fragilysin-3 prodomain-like › Fragilysin-3 prodomain › Fragilysin-3 prodomain | 0.59 | 44.0 | 3.48e-01 | 88.0% | 96.7% |
| 3789224 | 633.23.1.9 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 | 0.56 | 44.0 | 3.05e-01 | 94.0% | 31.2% |
| 3651531 | 387.1.1.0 ↗ | few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related | 0.56 | 36.0 | 3.82e-01 | 74.0% | 73.3% |
| 4120506 | 243.11.1.4 ↗ | a+b two layers › Cystatin-like › NP_346341.1 protein › NP_346341.1 protein › PF29632 | 0.55 | 45.0 | 3.94e-01 | 96.0% | 75.0% |
| 3613468 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.54 | 41.0 | 3.81e-01 | 84.0% | 69.2% |
| 3996079 | 2003.1.5.28 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › mRNA_G-N7_MeTrfase | 0.54 | 39.0 | 2.75e-01 | 84.0% | 24.0% |
| 3180421 | 239.1.1.0 ↗ | beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like | 0.53 | 42.0 | 3.92e-01 | 96.0% | 87.1% |
| 3895434 | 101.1.1.76 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 | 0.53 | 41.0 | 3.10e-01 | 84.0% | 55.8% |
| 4263140 | 325.1.7.0 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif | 0.53 | 39.0 | 3.63e-01 | 84.0% | 72.9% |
| 3559931 | 3850.1.1.1 ↗ | few secondary structure elements › Protein-only RNase P Zn-binding domain › Protein-only RNase P Zn-binding domain › Protein-only RNase P Zn-binding domain › PRORP | 0.53 | 35.0 | 3.26e-01 | 86.0% | 49.3% |
| 3859372 | 9.13.1.0 ↗ | beta barrels › Lipocalins/Streptavidin › AOC barrel-like › AOC barrel-like | 0.52 | 38.0 | 3.19e-01 | 86.0% | 64.8% |
| 3964606 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.52 | 43.0 | 3.06e-01 | 98.0% | 91.8% |
| 4954545 | 4056.1.1.0 ↗ | beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein | 0.52 | 39.0 | 3.26e-01 | 90.0% | 46.7% |
| 5018480 | 1104.1.1.0 ↗ | a+b complex topology › Helicase Cch N-terminal domain › Helicase Cch N-terminal domain › Helicase Cch N-terminal domain | 0.51 | 39.0 | 2.90e-01 | 100.0% | 54.4% |
| 5003452 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.50 | 37.0 | 2.89e-01 | 84.0% | 44.6% |
D3
medium
residues 314-366_405-453_536-561
D4
medium
residues 367-379_495-535
Domain cluster:
representative
CATH (17)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2c5iT00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.76 | 54.0 | 4.49e-01 | 75.9% | 72.3% |
| 2lmgA00 | 1.20.1270.10 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.74 | 53.0 | 4.78e-01 | 75.9% | 64.9% |
| 2wgmA01 | 1.20.20.10 | Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C | 0.73 | 53.0 | 4.58e-01 | 75.9% | 52.4% |
| 6ynwH01 | 1.20.20.10 | Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C | 0.73 | 52.0 | 4.68e-01 | 75.9% | 67.6% |
| 7s0rB01 | 1.20.81.20 | Mainly Alpha › Up-down Bundle › Receptor-associated Protein › | 0.72 | 51.0 | 4.60e-01 | 75.9% | 63.2% |
| 2p4vA01 | 1.10.287.180 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain | 0.70 | 49.0 | 4.45e-01 | 75.9% | 72.4% |
| 3ehfD01 | 1.20.5.1930 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.68 | 48.0 | 4.61e-01 | 75.9% | 92.1% |
| 1jalA03 | 1.10.150.300 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain | 0.67 | 47.0 | 4.19e-01 | 75.9% | 59.3% |
| 1txuA01 | 1.10.246.120 | Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › | 0.64 | 45.0 | 3.82e-01 | 75.9% | 57.4% |
| 3fblA00 | 1.20.58.800 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.63 | 45.0 | 3.98e-01 | 75.9% | 58.5% |
| 1wp7A00 | 1.10.287.770 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like | 0.63 | 43.0 | 4.17e-01 | 74.1% | 100.0% |
| 3h0dB02 | 1.10.1200.150 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Transcriptional repressor of class III stress genes, C-terminal domain | 0.61 | 53.0 | 4.68e-01 | 100.0% | 67.9% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.59 | 40.0 | 3.78e-01 | 72.2% | 95.5% |
| 8b6jF01 | 1.10.287.20 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain | 0.57 | 40.0 | 3.80e-01 | 75.9% | 65.7% |
| 1ugoA00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.57 | 42.0 | 3.68e-01 | 88.9% | 79.8% |
| 1sq5C00 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.54 | 46.0 | 2.91e-01 | 100.0% | 33.9% |
| 3onqA01 | 1.20.5.5100 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.52 | 36.0 | 4.00e-01 | 74.1% | 100.0% |
ECOD (7)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4178402 | 1054.1.1.1 ↗ | alpha bundles › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arg_decarbox_C | 0.74 | 53.0 | 3.40e-01 | 75.9% | 19.2% |
| 4929737 | 4144.1.1.0 ↗ | alpha duplicates or obligate multimers › YejL-like › YejL-like › YejL-like | 0.74 | 51.0 | 4.63e-01 | 74.1% | 56.0% |
| 2674763 | 5041.1.1.1 ↗ | extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C | 0.73 | 52.0 | 4.70e-01 | 75.9% | 66.7% |
| 3997639 | 7563.1.1.0 ↗ | a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related | 0.57 | 47.0 | 3.00e-01 | 100.0% | 59.7% |
| 3374875 | 101.1.1.359 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › DUF7746 | 0.55 | 43.0 | 4.32e-01 | 87.0% | 100.0% |
| 3374727 | 315.1.1.11 ↗ | a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › DUF7746 | 0.51 | 39.0 | 3.93e-01 | 88.9% | 94.5% |
| 3906715 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.51 | 40.0 | 3.57e-01 | 92.6% | 63.5% |
D5
medium
residues 454-494_562-685