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IMGVR_UViG_3300028628_000030-3300028628-Ga0302249_100069521

Arc-Vir

IMGVR_UViG_3300028628_000030-3300028628-Ga0302249_100069521

Identity

Kingdom:
archaea

Quality

84.4 mean pLDDT

Cluster

View cluster (66 members)

3D Structure

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Domains

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

D1 high residues 20-103
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 24.0 3.30e-05 88.1% 18.2%
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.87 81.0 5.85e-01 100.0% 61.5%
2gv9A03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.85 80.0 5.71e-01 100.0% 59.7%
2qxfA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.85 79.0 5.88e-01 100.0% 59.9%
4qclA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.82 76.0 5.16e-01 100.0% 52.4%
4fvmA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.81 75.0 5.33e-01 100.0% 64.5%
1u6gC00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.62 51.0 2.85e-01 90.5% 10.3%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.59 30.0 3.52e-01 91.7% 70.9%
1nzjA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 40.0 3.51e-01 100.0% 45.7%
2wvxA04 1.20.1610.10 Mainly Alpha › Up-down Bundle › Glycosyl hydrolase family fold › alpha-1,2-mannosidases domains 0.56 44.0 3.52e-01 85.7% 84.4%
4a0gC03 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 42.0 3.07e-01 85.7% 45.9%
4nxiA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 38.0 2.93e-01 75.0% 82.4%
4i6kA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.53 41.0 2.92e-01 84.5% 49.8%
6acsA00 3.40.1180.10 Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like 0.52 41.0 3.11e-01 88.1% 44.9%
3ufbA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 40.0 2.76e-01 85.7% 58.2%
1k6jB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 40.0 3.13e-01 86.9% 79.2%
2lxlA00 1.25.40.270 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 0.52 44.0 3.66e-01 100.0% 84.0%
5e0sB00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.51 42.0 3.26e-01 92.9% 77.6%
1c4oA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 3.32e-01 85.7% 66.7%
4ijaA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 41.0 3.45e-01 90.5% 92.7%
2p0tA02 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.50 29.0 3.13e-01 70.2% 66.7%
5hn3A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.50 39.0 2.69e-01 86.9% 29.2%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 42.0 2.78e-01 97.6% 58.7%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5055213 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.88 84.0 6.20e-01 100.0% 45.0%
4932479 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.88 83.0 5.46e-01 100.0% 36.4%
4952383 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.87 79.0 5.33e-01 100.0% 30.2%
None — 0.87 81.0 5.15e-01 100.0% 36.4%
None — 0.87 82.0 4.58e-01 100.0% 14.4%
None — 0.87 81.0 4.59e-01 100.0% 15.0%
3584771 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.87 81.0 5.39e-01 100.0% 40.7%
3710418 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 81.0 5.10e-01 100.0% 35.5%
3798596 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.86 81.0 5.76e-01 100.0% 53.3%
4939488 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 81.0 5.39e-01 100.0% 35.5%
4649118 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.86 81.0 5.06e-01 100.0% 30.4%
4992857 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.86 81.0 5.89e-01 100.0% 42.4%
3619240 304.48.1.59 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.86 81.0 4.60e-01 100.0% 15.8%
4988803 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 81.0 5.05e-01 100.0% 28.1%
3802227 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.86 81.0 4.54e-01 100.0% 14.2%
4953654 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 81.0 5.18e-01 100.0% 33.2%
3605750 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 81.0 4.49e-01 100.0% 13.2%
3266685 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 80.0 4.39e-01 100.0% 10.3%
4504110 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.86 80.0 4.97e-01 100.0% 26.5%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 80.0 5.23e-01 100.0% 32.2%
5056578 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 80.0 5.32e-01 100.0% 38.0%
1822623 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 80.0 5.40e-01 100.0% 48.2%
5067181 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 80.0 4.94e-01 100.0% 27.0%
3941572 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 79.0 5.12e-01 100.0% 35.0%
5029084 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 79.0 5.63e-01 100.0% 48.4%
5039400 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 79.0 5.25e-01 100.0% 34.0%
4982659 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 79.0 5.05e-01 100.0% 27.7%
4942685 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.84 79.0 4.75e-01 100.0% 22.9%
5076410 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 79.0 4.98e-01 100.0% 26.5%
5023018 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 78.0 5.66e-01 100.0% 62.4%
3604297 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.84 74.0 5.66e-01 100.0% 45.1%
4432985 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 79.0 5.78e-01 100.0% 51.0%
4282509 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 78.0 4.60e-01 100.0% 20.0%
4990754 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 77.0 5.53e-01 100.0% 43.6%
4956223 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 77.0 5.14e-01 100.0% 35.6%
4966854 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 77.0 4.94e-01 100.0% 27.2%
5043498 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 77.0 4.85e-01 100.0% 26.7%
3256261 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 77.0 5.33e-01 100.0% 53.3%
4492006 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 78.0 5.26e-01 100.0% 34.8%
5063605 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 77.0 4.94e-01 100.0% 28.3%
5036329 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.82 77.0 5.42e-01 100.0% 40.0%
5073475 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.82 77.0 5.06e-01 100.0% 31.3%
5073666 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.81 75.0 4.89e-01 100.0% 35.8%
4981192 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.81 75.0 5.19e-01 100.0% 40.8%
5040509 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.80 74.0 4.80e-01 100.0% 28.4%
5025208 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.80 74.0 5.26e-01 100.0% 44.3%
3893443 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.78 71.0 5.18e-01 100.0% 50.5%
5044376 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.77 70.0 4.63e-01 100.0% 33.8%
3683989 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.70 65.0 4.73e-01 100.0% 48.6%
3920705 2005.1.1.7 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.59 46.0 3.32e-01 86.9% 72.3%
3509753 573.1.1.0 ↗ alpha duplicates or obligate multimers › Soluble domain of poliovirus core protein 3a › Soluble domain of poliovirus core protein 3a › Soluble domain of poliovirus core protein 3a 0.58 29.0 3.73e-01 85.7% 97.4%
4934213 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.56 41.0 3.62e-01 78.6% 93.1%
4492394 2005.1.1.7 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.56 44.0 3.07e-01 85.7% 86.8%
None — 0.55 43.0 2.68e-01 86.9% 36.7%
5061423 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.54 48.0 3.20e-01 100.0% 51.9%
None — 0.54 44.0 2.72e-01 91.7% 82.2%
4431536 2007.1.7.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Rossmann-like domain in dehydroquinate synthase-like enzymes › DHQ_synthase 0.54 42.0 3.46e-01 88.1% 72.9%
5062136 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.54 44.0 3.52e-01 90.5% 84.7%
3707575 2484.1.1.74 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Tex_YqgF 0.53 42.0 3.49e-01 94.0% 46.9%
4302854 7510.1.1.1 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Iso_dh 0.51 41.0 3.50e-01 88.1% 82.9%
D2 high residues 115-165
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a7wA00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.75 57.0 5.12e-01 80.4% 76.5%
1k82A02 1.10.8.50 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.71 51.0 3.89e-01 78.4% 59.3%
7ztbB01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.70 48.0 3.37e-01 72.5% 38.7%
6f0cA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.68 58.0 3.47e-01 96.1% 42.6%
2bvlA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 51.0 4.23e-01 100.0% 75.6%
4uqfG01 1.10.286.10 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › GTP cyclohydrolase I, N-terminal domain 0.55 39.0 3.89e-01 76.5% 75.0%
1zbuB01 1.10.720.30 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › SAP domain 0.54 45.0 4.05e-01 96.1% 83.8%
2ziwB02 1.10.150.670 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Crossover junction endonuclease EME1, DNA-binding domain 0.53 37.0 3.03e-01 76.5% 38.8%
4impA01 6.10.140.1830 Special › Helix non-globular › Helix Hairpins › 0.52 39.0 3.89e-01 88.2% 83.0%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None — 0.71 62.0 4.15e-01 100.0% 72.2%
3483114 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.71 57.0 4.80e-01 88.2% 83.5%
3273602 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.68 50.0 4.93e-01 78.4% 98.2%
3446951 101.1.1.3 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding 0.66 53.0 4.39e-01 90.2% 50.0%
3939282 650.1.1.10 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › PF30912 0.62 43.0 3.78e-01 72.5% 46.7%
996952 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.62 45.0 3.86e-01 78.4% 47.1%
3583564 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.59 45.0 4.17e-01 90.2% 74.3%
3638810 2484.1.1.109 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › bVLRF1 0.56 47.0 3.23e-01 92.2% 38.8%
4011063 327.5.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins 0.55 47.0 3.47e-01 96.1% 49.6%
3491643 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.54 44.0 4.29e-01 96.1% 81.8%