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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_narna-like_virus_21

RNA-dependent_RNA_polymerase__YP_009337775__Hubei_narna-like_virus_21__1922952

Identity

Accession:
YP_009337775 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

67.8 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 1-98
PDB
Domain cluster: representative
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iqcA00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.64 39.0 3.69e-01 82.7% 50.4%
3lnnB03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.61 39.0 4.57e-01 79.6% 94.0%
3i01A01 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 45.0 3.66e-01 77.6% 62.1%
1aluA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.60 36.0 3.09e-01 81.6% 36.9%
3qx3A04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.60 43.0 4.27e-01 73.5% 99.0%
1abvA00 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.60 42.0 4.18e-01 73.5% 82.9%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.58 36.0 3.78e-01 81.6% 67.4%
6lccA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.58 45.0 3.05e-01 83.7% 25.8%
2m6bA00 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.57 42.0 3.71e-01 78.6% 98.0%
1jqkA03 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.57 41.0 3.41e-01 75.5% 63.4%
1hm7B00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 45.0 3.20e-01 85.7% 31.1%
3d85C00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 41.0 3.74e-01 76.5% 99.2%
6kd7A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 46.0 3.16e-01 88.8% 55.7%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.55 37.0 3.20e-01 85.7% 43.8%
2pbeA02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.54 38.0 3.53e-01 73.5% 84.9%
4hz4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.50 44.0 4.20e-01 94.9% 92.9%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5058148 601.4.1.0 alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.63 48.0 4.77e-01 78.6% 99.0%
3282529 632.1.1.3 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.58 34.0 3.35e-01 79.6% 53.3%
3441715 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.55 43.0 4.13e-01 84.7% 72.7%
3962961 150.5.1.53 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PPE 0.55 42.0 4.61e-01 78.6% 96.2%
3957966 150.8.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE › PPE 0.54 41.0 3.87e-01 78.6% 67.0%
4017135 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.52 30.0 3.07e-01 81.6% 58.9%
3954841 150.5.1.11 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › T7SS_ESX_EspC 0.52 40.0 4.00e-01 79.6% 79.0%
3979729 3755.3.1.500 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › IpaC_SipC 0.52 41.0 3.79e-01 82.7% 80.0%
3284573 150.5.1.11 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › T7SS_ESX_EspC 0.51 39.0 3.92e-01 79.6% 79.0%
3781441 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.51 39.0 3.97e-01 79.6% 89.5%
5014397 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 0.50 38.0 3.13e-01 81.6% 64.2%
D2 medium residues 99-109_287-311_349-380
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4epzA00 1.25.40.810 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › UpxZ 0.64 39.0 2.97e-01 100.0% 27.3%
1ct5A00 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.58 42.0 2.92e-01 76.5% 38.2%
1gq2A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 39.0 2.68e-01 79.4% 85.3%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 36.0 3.08e-01 100.0% 40.7%
2zj2A04 1.10.3380.20 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.55 44.0 3.31e-01 88.2% 39.5%
5ix8A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 43.0 3.39e-01 91.2% 95.0%
3anwB00 1.20.58.2050 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 40.0 3.06e-01 82.4% 81.5%
1zoyA03 1.20.58.100 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain 0.51 38.0 3.29e-01 82.4% 77.8%
3p01A01 6.10.140.590 Special › Helix non-globular › Helix Hairpins › 0.51 39.0 3.61e-01 98.5% 66.3%
3ajfA00 1.20.1440.190 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tenuivirus movement protein 0.50 37.0 3.38e-01 79.4% 64.1%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3684651 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 0.63 36.0 3.37e-01 73.5% 47.1%
5049338 2007.1.4.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain › DAGK_cat 0.56 42.0 3.44e-01 79.4% 60.0%
3677130 103.1.1.34 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PIR2-like_helical 0.54 41.0 3.33e-01 82.4% 92.6%
3343812 7073.1.1.1 alpha arrays › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › Malic_M 0.51 36.0 3.14e-01 100.0% 48.6%
3638639 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.51 39.0 3.43e-01 82.4% 68.0%
3214991 101.1.2.10 alpha arrays › HTH › HTH › winged helix domain › Linker_histone 0.51 40.0 3.79e-01 100.0% 70.6%
D3 medium residues 110-165_177-251_312-348
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5mmjo00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.54 21.0 3.11e-01 72.6% 78.7%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2850105 304.48.1.19 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Bunya_RdRp 0.63 46.0 3.94e-01 75.6% 64.9%
4152428 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.60 53.0 4.12e-01 93.5% 54.1%
3589612 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.59 55.0 4.36e-01 99.4% 60.0%
4138932 304.48.1.72 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_N 0.58 49.0 3.97e-01 88.7% 62.3%
3173834 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.58 53.0 3.93e-01 98.8% 45.6%
4004424 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 53.0 4.04e-01 99.4% 52.0%
4497954 304.48.1.73 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1, RVT_N 0.57 53.0 4.26e-01 98.8% 62.9%
3945039 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 53.0 4.16e-01 99.4% 57.0%
4872037 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 47.0 3.99e-01 86.9% 65.8%
5029718 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 47.0 3.67e-01 86.9% 54.7%
4461237 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.56 52.0 3.64e-01 99.4% 36.3%
5002351 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.56 51.0 3.89e-01 97.6% 50.7%
5018583 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.55 51.0 4.10e-01 98.8% 59.0%
5018572 304.48.1.72 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_N 0.50 41.0 4.07e-01 86.3% 84.4%
D4 medium residues 252-286_381-522
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 38.0 4.79e-01 88.1% 97.2%
4mz0B05 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.57 23.0 3.75e-01 77.4% 100.0%
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.56 24.0 3.62e-01 78.5% 93.3%
1zpwX00 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 25.0 3.62e-01 81.9% 92.7%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.54 24.0 3.55e-01 78.5% 98.6%
1h3dA03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 22.0 3.42e-01 77.4% 100.0%
2ewhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.52 26.0 3.73e-01 80.2% 100.0%
2iboA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 27.0 3.76e-01 80.2% 100.0%
3d68A01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.52 26.0 3.49e-01 81.9% 91.3%
1vk8A00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 27.0 3.69e-01 80.2% 98.9%
1kwmA01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.51 25.0 3.43e-01 79.7% 94.3%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4944359 304.56.1.0 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.58 26.0 3.73e-01 80.8% 89.4%
4235667 304.56.1.2 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.57 26.0 3.74e-01 81.4% 90.6%
4507546 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.57 24.0 3.78e-01 76.3% 100.0%
4123628 304.56.1.2 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.57 26.0 3.81e-01 80.8% 96.2%
5007506 304.5.1.0 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.56 25.0 3.52e-01 78.0% 85.9%
4279811 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.56 24.0 3.49e-01 76.8% 87.5%
4502075 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.56 23.0 3.70e-01 80.2% 100.0%
4936417 304.26.1.3 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › DUF2102 0.55 29.0 3.64e-01 83.1% 83.8%
4070496 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.55 24.0 3.58e-01 79.1% 96.0%
3395435 304.11.1.0 a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.55 23.0 3.53e-01 76.3% 100.0%
4231349 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.54 24.0 3.55e-01 78.0% 100.0%
4295716 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.54 24.0 3.54e-01 77.4% 100.0%
5023503 304.110.1.0 a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like 0.53 23.0 3.45e-01 77.4% 98.6%
4156338 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.52 23.0 3.39e-01 78.5% 96.0%
3927365 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.51 39.0 3.50e-01 95.5% 57.6%
3643305 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.50 37.0 4.26e-01 84.7% 100.0%
D5 medium residues 536-616
PDB