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RdRp

Euk-Vir

Hubei_permutotetra-like_virus_8

RdRp__YP_009337703__Hubei_permutotetra-like_virus_8__1923082

Identity

Accession:
YP_009337703 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

65.4 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 896-1005
PDB
D2 medium residues 16-46_552-712
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D29-60_540-665
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22260.2 best Permu_RdRp_thumb 104.3 4.80e-30 56.2% 100.0%
D3 medium residues 47-121_138-180_278-291
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1699894 304.48.2.2 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Permu_RdRp_palm 0.86 82.0 5.26e-01 100.0% 44.1%
D4 medium residues 329-388
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 49.2 5.10e-13 100.0% 16.8%
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6pxcA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.67 56.0 4.72e-01 100.0% 53.8%
1ym5A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.65 52.0 3.92e-01 91.7% 53.2%
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.65 46.0 3.54e-01 81.7% 33.3%
7q04F01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.64 45.0 3.76e-01 75.0% 43.1%
3buxB03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.62 51.0 4.60e-01 96.7% 65.1%
3k2tA01 3.30.505.50 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain 0.61 44.0 4.85e-01 88.3% 100.0%
6j7xC01 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.61 45.0 3.57e-01 83.3% 39.3%
7szeB01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.60 42.0 3.52e-01 75.0% 41.1%
2lojA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.60 37.0 4.18e-01 90.0% 94.9%
2xp1A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.59 48.0 4.14e-01 100.0% 56.8%
1kvzA00 3.10.130.10 Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain 0.59 50.0 4.15e-01 95.0% 74.8%
1vr8A00 3.40.1000.20 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › TM1622-like 0.59 42.0 3.26e-01 75.0% 59.3%
7jooC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 44.0 3.73e-01 81.7% 52.6%
2gu1A01 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 48.0 4.28e-01 95.0% 97.7%
3a0oA03 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.57 47.0 3.03e-01 90.0% 69.4%
4gw9A02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 42.0 3.69e-01 80.0% 57.6%
5jk0B01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.56 41.0 2.98e-01 76.7% 80.3%
2pm6D01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 42.0 2.79e-01 83.3% 50.0%
1q15A01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.55 47.0 3.30e-01 98.3% 73.7%
6i8xA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 39.0 3.01e-01 76.7% 45.6%
2dbuB00 3.60.20.40 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Gamma-glutamyltranspeptidase, small (S) subunit 0.55 44.0 3.09e-01 88.3% 95.3%
3ed3A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 46.0 3.79e-01 100.0% 81.0%
3h74A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.54 48.0 3.11e-01 100.0% 48.9%
5tf2A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 46.0 2.93e-01 98.3% 96.7%
5yjwA00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.54 45.0 2.76e-01 100.0% 26.0%
1zswA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.54 41.0 2.98e-01 83.3% 50.6%
7snsB01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 47.0 3.43e-01 96.7% 35.8%
1nbwA04 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 41.0 3.32e-01 90.0% 94.7%
1gqyB02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.53 45.0 3.13e-01 100.0% 63.1%
1epwA03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 43.0 3.03e-01 100.0% 75.1%
4huzA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 40.0 2.96e-01 83.3% 56.6%
2oq8A00 2.60.40.2930 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 42.0 3.26e-01 95.0% 92.7%
3nixB00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 46.0 2.79e-01 100.0% 68.5%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 44.0 3.09e-01 95.0% 59.2%
3bn8A00 3.30.1050.10 Alpha Beta › 2-Layer Sandwich › Nonspecific Lipid-transfer Protein; Chain A › SCP2 sterol-binding domain 0.51 39.0 3.25e-01 85.0% 50.0%
3v0aB03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 44.0 3.10e-01 100.0% 54.1%
4zpjA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 42.0 3.18e-01 100.0% 52.0%
6hoxA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 42.0 2.93e-01 100.0% 75.9%
4jglA00 2.40.128.530 Mainly Beta › Beta Barrel › Lipocalin › 0.50 44.0 3.32e-01 100.0% 40.8%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3585186 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.72 42.0 4.93e-01 80.0% 97.1%
3937472 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.71 55.0 4.60e-01 100.0% 48.6%
4971351 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.69 48.0 3.86e-01 73.3% 38.3%
2858693 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.68 48.0 5.23e-01 78.3% 89.8%
3698579 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.67 47.0 3.87e-01 73.3% 50.0%
2856288 66.1.1.1 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain › Rieske 0.67 44.0 5.06e-01 78.3% 100.0%
4964362 6030.1.1.1 ↗ a+b two layers › Middle domain of ribosomal protein S2-related protein › Middle domain of ribosomal protein S2-related protein › Middle domain of ribosomal protein S2-related protein › DR2241 0.66 49.0 3.92e-01 80.0% 75.8%
1732311 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.65 46.0 4.25e-01 80.0% 58.2%
4487967 66.1.1.1 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain › Rieske 0.64 44.0 3.79e-01 83.3% 44.0%
2719643 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.63 46.0 4.13e-01 80.0% 56.1%
1150523 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.63 45.0 4.07e-01 78.3% 55.6%
5042256 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.61 41.0 3.52e-01 70.0% 64.6%
3534391 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.61 46.0 3.20e-01 96.7% 25.3%
5077119 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 46.0 3.52e-01 83.3% 36.7%
3825338 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 46.0 3.62e-01 83.3% 39.3%
5074455 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.60 47.0 3.93e-01 86.7% 48.2%
None — 0.60 42.0 2.62e-01 73.3% 65.7%
5019949 4294.1.1.1 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › Rieske 0.60 44.0 3.80e-01 98.3% 49.5%
4236690 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.59 46.0 4.36e-01 86.7% 82.4%
3282813 268.1.1.0 ↗ a+b two layers › Sterol carrier protein-like › Sterol carrier protein, SCP-related › Sterol carrier protein, SCP-related 0.59 44.0 4.00e-01 81.7% 60.0%
5022798 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.59 46.0 2.72e-01 86.7% 25.5%
3189694 9.1.1.33 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF1365 0.58 51.0 3.33e-01 100.0% 44.3%
3883146 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.58 39.0 4.31e-01 73.3% 91.1%
3694123 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.55 48.0 2.94e-01 100.0% 63.9%
4930189 1.1.9.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.54 43.0 4.33e-01 93.3% 91.7%
3291166 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.54 47.0 3.98e-01 100.0% 61.0%
3924241 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 47.0 2.66e-01 100.0% 47.2%
3444338 10.1.1.35 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_3 0.53 45.0 3.02e-01 100.0% 44.9%
3427055 5.1.11.13 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › Beta-prop_RIC1_2nd 0.53 43.0 2.45e-01 93.3% 17.6%
5006258 205.1.1.128 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › APS-reductase_C 0.52 43.0 3.25e-01 100.0% 37.2%
4030034 109.4.1.1140 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_PEP5_VPS11 0.52 44.0 2.64e-01 100.0% 18.4%
4833287 205.1.1.35 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4+Fer4_7 0.52 43.0 3.71e-01 96.7% 87.1%
4204975 12.3.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Hepar_II_III 0.51 39.0 2.53e-01 90.0% 65.4%
5482 205.1.1.47 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4, APS-reductase_C, Fer4_7 0.51 42.0 3.17e-01 100.0% 36.2%
2512825 10.1.1.25 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Toxin_R_bind_N 0.51 42.0 2.94e-01 100.0% 77.9%
3211804 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.50 41.0 2.83e-01 100.0% 54.5%
4999777 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.50 42.0 2.88e-01 100.0% 80.2%
5038962 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 36.0 4.01e-01 93.3% 97.8%
1570612 10.1.1.25 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Toxin_R_bind_N 0.50 43.0 3.03e-01 100.0% 53.6%