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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_narna-like_virus_3

RNA-dependent_RNA_polymerase__YP_009337787__Hubei_narna-like_virus_3__1922957

Identity

Accession:
YP_009337787 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.8 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 5-115
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hb0D01 1.20.120.1880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleoporin, helical C-terminal domain 0.71 34.0 2.58e-01 84.7% 20.7%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 32.0 3.78e-01 95.5% 65.4%
2vxgA02 1.10.220.100 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › conserved c-terminal region of ge- 1 0.63 29.0 3.29e-01 79.3% 55.3%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 34.0 3.07e-01 90.1% 40.9%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.58 34.0 3.61e-01 93.7% 62.7%
2a0uB01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.58 49.0 4.40e-01 93.7% 95.0%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.57 34.0 3.60e-01 93.7% 65.0%
3vprA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 41.0 3.80e-01 76.6% 80.0%
1iufA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.56 38.0 4.30e-01 75.7% 98.7%
3frqB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 45.0 3.85e-01 89.2% 58.2%
8gccA03 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.55 38.0 3.99e-01 73.0% 82.7%
3f4mA00 1.20.1440.160 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like 0.54 39.0 3.53e-01 74.8% 69.5%
4hhyC01 1.20.142.10 Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › Poly(ADP-ribose) polymerase, regulatory domain 0.53 35.0 3.37e-01 82.9% 55.7%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 34.0 3.21e-01 95.5% 52.2%
1nklA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.53 36.0 4.18e-01 78.4% 100.0%
5k7fA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 37.0 3.55e-01 74.8% 78.3%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 36.0 3.54e-01 93.7% 65.0%
3iqtA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.53 40.0 4.05e-01 82.0% 84.2%
1xzpA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.52 41.0 3.59e-01 82.9% 69.9%
4q6bA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 41.0 3.45e-01 86.5% 83.6%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.50 39.0 3.21e-01 82.0% 89.5%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.50 45.0 3.65e-01 100.0% 56.3%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3570499 604.1.1.95 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › KIAA1755_C 0.73 32.0 3.45e-01 89.2% 48.4%
3717612 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 0.67 39.0 2.99e-01 100.0% 25.1%
3175091 1002.1.1.1 alpha complex topology › Fluoride ion channel › Fluoride ion channel › Fluoride ion channel › CRCB 0.64 37.0 3.16e-01 97.3% 36.0%
3257705 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.63 34.0 3.70e-01 94.6% 62.1%
3637195 142.1.1.0 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.63 37.0 3.85e-01 80.2% 63.0%
3988387 604.10.1.1 alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac › PTS_IIA 0.62 32.0 3.43e-01 89.2% 57.0%
5055566 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.62 36.0 3.64e-01 93.7% 57.4%
4954611 1079.1.1.19 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › DUF2162 0.61 54.0 4.58e-01 100.0% 73.2%
4397328 604.10.1.1 alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac › PTS_IIA 0.58 34.0 3.46e-01 92.8% 57.3%
3829773 3684.1.1.2 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › BPS1 0.55 42.0 3.31e-01 79.3% 68.4%
3337686 5086.1.1.64 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › Sin3_corepress 0.54 40.0 3.98e-01 82.0% 73.3%
3617266 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 0.54 37.0 3.62e-01 95.5% 65.0%
4028766 181.1.1.1 alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.54 40.0 4.37e-01 82.0% 100.0%
4535860 5048.1.1.1 alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like › MIP 0.54 42.0 3.13e-01 83.8% 54.2%
4103475 140.1.1.0 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.53 38.0 3.21e-01 74.8% 54.7%
4013477 1025.1.1.0 alpha bundles › Stonustoxin helical domain › Stonustoxin helical domain › Stonustoxin helical domain 0.52 35.0 3.58e-01 100.0% 69.1%
5060908 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.52 42.0 3.81e-01 86.5% 81.8%
3626983 310.2.1.2 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › MIX23 0.52 36.0 3.47e-01 89.2% 62.9%
4096325 108.1.1.104 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5, EF-hand_8 0.52 45.0 3.13e-01 95.5% 32.7%
3708405 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.52 42.0 3.83e-01 88.3% 99.3%
3276216 5048.1.1.1 alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like › MIP 0.52 43.0 3.44e-01 91.0% 100.0%
1407186 3832.1.1.1 alpha bundles › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › DUF758 0.52 36.0 3.10e-01 72.1% 58.6%
4285641 138.1.1.2 alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › Rep_fac_C 0.51 36.0 3.87e-01 85.6% 84.2%
3834068 5050.1.1.8 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › FPN1 0.51 42.0 3.39e-01 89.2% 83.9%
4442857 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 42.0 3.50e-01 89.2% 90.3%
3386452 5050.1.1.21 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › FTR1 0.51 44.0 4.03e-01 98.2% 73.8%
5074065 632.11.1.18 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF5658 0.50 33.0 3.48e-01 100.0% 74.5%
D2 medium residues 116-210
PDB
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2uxwA01 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 37.0 2.94e-01 87.4% 30.6%
4l7aA00 3.40.390.70 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › 0.56 42.0 3.11e-01 80.0% 42.1%
5j1hA01 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 39.0 3.19e-01 96.8% 39.6%
2yufA00 1.20.120.2010 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NAB conserved domain 2 0.53 35.0 3.12e-01 92.6% 45.1%
1zvuA03 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.51 40.0 3.54e-01 84.2% 60.7%
2rq1A00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.51 38.0 3.69e-01 82.1% 70.6%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3477262 3684.1.1.0 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.62 48.0 4.01e-01 85.3% 89.7%
3446958 109.4.1.349 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIX1 0.61 54.0 3.79e-01 100.0% 48.1%
2462953 1075.4.1.1 alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.60 39.0 2.60e-01 84.2% 19.3%
5045553 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.57 45.0 2.88e-01 85.3% 41.3%
3727312 192.2.1.6 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_3 0.57 46.0 4.38e-01 86.3% 80.0%
5040873 4271.1.1.3 alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.56 43.0 3.33e-01 82.1% 87.0%
3965710 5050.1.1.53 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MarC 0.56 49.0 3.90e-01 100.0% 77.6%
5025741 3896.1.2.6 alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-archaeol synthase › DUF92 0.55 41.0 3.71e-01 77.9% 95.4%
3942760 1079.1.1.8 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › LysE 0.54 47.0 3.73e-01 100.0% 76.1%
3227022 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 30.0 3.19e-01 98.9% 60.0%
3489265 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.53 44.0 3.31e-01 94.7% 89.6%
4192 4970.1.1.0 alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.52 42.0 4.07e-01 87.4% 79.2%
3448303 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.52 37.0 2.69e-01 76.8% 38.7%
4190659 2500.1.1.2 a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.51 43.0 2.62e-01 96.8% 58.1%
3413139 3542.1.1.3 alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Peptidase_A22B 0.50 39.0 2.73e-01 84.2% 91.9%
D3 medium residues 211-235_277-394
PDB
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.52 47.0 3.18e-01 97.2% 33.9%
2qlvB02 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.52 16.0 2.87e-01 87.4% 97.4%
8gccA02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.52 20.0 2.58e-01 88.8% 55.8%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3615272 304.48.1.25 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.50 38.0 2.80e-01 82.5% 29.4%
D4 medium residues 395-438_481-586
PDB
D5 medium residues 587-665
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l3lA01 1.20.58.1250 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Tubulin Binding Cofactor C, N-terminal domain 0.64 52.0 4.80e-01 92.4% 72.6%
2yinA03 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.62 51.0 4.48e-01 96.2% 97.7%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 45.0 4.86e-01 89.9% 100.0%
3zheA02 1.25.40.760 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.61 52.0 3.95e-01 100.0% 43.5%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.60 48.0 4.40e-01 91.1% 76.4%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.58 46.0 4.32e-01 92.4% 68.9%
3t9oB00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.58 47.0 4.16e-01 91.1% 70.8%
3urzA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 46.0 3.56e-01 91.1% 41.6%
2kmfA01 1.20.58.810 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Photosystem II Pbs27 0.57 45.0 4.23e-01 91.1% 72.5%
3cllA00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.56 48.0 3.52e-01 100.0% 89.6%
1zu2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 47.0 3.84e-01 98.7% 49.4%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.51 35.0 3.63e-01 73.4% 100.0%
2xrhA00 1.20.120.1430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HP0721 helical bundle 0.50 41.0 3.79e-01 89.9% 80.0%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3909538 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 51.0 4.76e-01 92.4% 93.3%
3780747 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 46.0 3.40e-01 100.0% 30.0%
3574716 109.4.1.1312 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30475 0.58 41.0 3.96e-01 97.5% 63.2%
5005973 3625.1.1.0 alpha bundles › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain 0.58 40.0 3.89e-01 84.8% 64.4%
5016158 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 45.0 3.80e-01 100.0% 49.3%
4642819 601.7.1.61 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › PF27473 0.53 39.0 3.22e-01 81.0% 82.6%
D6 medium residues 666-832
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.53 23.0 2.87e-01 71.9% 62.0%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None 0.53 37.0 2.96e-01 71.3% 79.2%