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DNA_polymerase

Euk-Vir

Spodoptera_littoralis_nucleopolyhedrovirus

DNA_polymerase__YP_009505872__Spodoptera_littoralis_nucleopolyhedrovirus__10456

Identity

Accession:
YP_009505872 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

81.2 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.

D2 medium residues 208-277
PDB
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1q8iA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.84 64.0 4.56e-01 100.0% 30.3%
1hfeL03 3.40.950.10 Alpha Beta › 3-Layer(aba) Sandwich › Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 › Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 0.66 45.0 3.60e-01 71.4% 35.7%
5o5jC01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.64 44.0 4.02e-01 70.0% 62.2%
1ez0A02 3.40.309.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 0.60 50.0 3.65e-01 90.0% 90.8%
4i5tB00 3.30.428.70 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › ATP adenylyltransferase 0.60 48.0 3.16e-01 88.6% 87.2%
4dg8A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.59 47.0 4.31e-01 87.1% 71.7%
3n9vB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.59 43.0 2.82e-01 75.7% 69.2%
7r7eA01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.58 47.0 4.02e-01 90.0% 68.9%
2kdnA00 3.30.300.90 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › BolA-like 0.58 45.0 3.94e-01 84.3% 85.2%
2dewX03 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.58 45.0 2.94e-01 90.0% 84.1%
2imqX00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.58 41.0 2.75e-01 75.7% 23.2%
4ic1D00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.57 43.0 3.12e-01 81.4% 72.3%
3rvaA01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.57 50.0 3.92e-01 100.0% 57.7%
6o6eB02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.57 45.0 3.97e-01 87.1% 68.2%
2d8bA01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 46.0 3.84e-01 95.7% 59.3%
3laxA00 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.57 44.0 3.87e-01 84.3% 87.7%
2vsqA06 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.57 45.0 3.97e-01 87.1% 66.7%
3kxwA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.57 45.0 3.77e-01 87.1% 66.1%
3bioA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.56 46.0 3.93e-01 90.0% 75.4%
1m4jA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 46.0 3.82e-01 94.3% 63.2%
2f9iD00 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 0.56 46.0 3.29e-01 100.0% 96.9%
3tghA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.55 48.0 3.18e-01 100.0% 51.7%
2y27A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.54 44.0 3.95e-01 91.4% 75.7%
4c89C00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 46.0 3.04e-01 100.0% 82.6%
1wduB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 44.0 3.24e-01 97.1% 94.1%
1v7wA02 2.60.420.10 Mainly Beta › Sandwich › Maltose phosphorylase, domain 3 › Maltose phosphorylase, domain 3 0.53 37.0 3.54e-01 72.9% 92.9%
6vhvA01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 42.0 3.88e-01 87.1% 74.2%
4oc8A02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.53 41.0 3.29e-01 91.4% 75.6%
2v7bA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 42.0 3.81e-01 88.6% 77.3%
3ajvC02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.52 40.0 3.80e-01 88.6% 89.0%
1t71A00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.52 43.0 3.01e-01 98.6% 74.0%
4qtpD00 3.30.750.24 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › STAS domain 0.52 43.0 3.66e-01 91.4% 93.9%
4gnxB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 39.0 3.37e-01 84.3% 91.8%
4dunA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.52 40.0 3.46e-01 90.0% 91.3%
2ookA00 3.40.50.10600 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SpoIIaa-like domains 0.51 40.0 3.49e-01 94.3% 96.8%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3404726 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 71.0 4.57e-01 100.0% 25.8%
3606428 2484.1.1.34 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.75 69.0 4.70e-01 100.0% 31.5%
3256261 2484.1.1.34 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.74 68.0 4.52e-01 100.0% 32.2%
4026339 5104.1.1.3 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA2 0.71 59.0 4.59e-01 90.0% 92.6%
4980263 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.65 44.0 4.28e-01 70.0% 76.2%
3743726 327.5.1.7 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 › Mug62 0.63 50.0 3.97e-01 87.1% 66.9%
4827484 327.5.1.6 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 › AMP-dom_DIP2-like 0.63 50.0 4.53e-01 88.6% 80.6%
3566342 327.5.1.7 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 › Mug62 0.62 50.0 4.01e-01 88.6% 58.6%
3960804 327.5.1.2 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 › AMP-binding_C 0.61 50.0 4.01e-01 88.6% 54.8%
3710133 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.61 45.0 3.66e-01 80.0% 55.7%
3880343 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 0.61 49.0 3.96e-01 91.4% 56.6%
4024668 2004.1.1.211 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CLP1_P 0.60 43.0 2.98e-01 75.7% 94.6%
4106936 327.5.1.2 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 › AMP-binding_C 0.60 49.0 4.36e-01 88.6% 75.0%
4010862 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 0.60 47.0 3.97e-01 82.9% 75.7%
3997846 207.1.1.142 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1, LRR_4, LRR_6, LRR_8 0.60 40.0 2.46e-01 70.0% 11.3%
4594294 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.60 47.0 4.27e-01 85.7% 75.8%
3290102 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 0.60 49.0 4.15e-01 91.4% 66.7%
3955921 327.5.1.6 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 › AMP-dom_DIP2-like 0.60 48.0 4.16e-01 88.6% 69.1%
3610560 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.59 46.0 3.98e-01 85.7% 68.7%
3867661 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.59 51.0 3.19e-01 98.6% 73.4%
3289450 327.5.1.6 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 › AMP-dom_DIP2-like 0.59 49.0 4.11e-01 91.4% 68.3%
3545493 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.59 49.0 3.83e-01 92.9% 51.0%
5051077 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.59 44.0 4.05e-01 80.0% 74.4%
None 0.59 46.0 3.82e-01 92.9% 93.8%
3530470 232.1.1.3 a+b duplicates or obligate multimers › Pentein › Pentein › Pentein › PAD 0.58 46.0 2.97e-01 91.4% 84.5%
10585 7556.1.1.1 a/b three-layered sandwiches › Fe-only hydrogenase › Fe-only hydrogenase › Fe-only hydrogenase › Fe_hyd_lg_C 0.58 42.0 2.77e-01 75.7% 17.8%
3277889 327.5.1.6 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 › AMP-dom_DIP2-like 0.58 48.0 4.13e-01 91.4% 72.2%
3966350 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 0.58 46.0 4.09e-01 87.1% 64.8%
3945514 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 42.0 2.92e-01 78.6% 93.4%
4442936 2484.3.1.5 mixed a+b and a/b › Ribonuclease H-like › Creatinase/prolidase N-terminal domain › Creatinase/prolidase N-terminal domain › PepQ_N 0.58 48.0 3.79e-01 94.3% 54.8%
4936587 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 51.0 3.43e-01 100.0% 28.2%
3503356 224.1.1.0 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.58 47.0 4.35e-01 97.1% 69.5%
1889960 7524.1.1.0 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like 0.58 39.0 2.76e-01 71.4% 58.5%
3954285 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.57 49.0 3.12e-01 98.6% 66.8%
4926924 2003.1.1.27 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › PDH_N 0.57 48.0 3.60e-01 95.7% 56.2%
3969404 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 0.57 46.0 3.81e-01 90.0% 60.8%
3219454 2484.1.1.190 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FBA_2 0.57 46.0 3.20e-01 91.4% 26.4%
4981292 7584.1.1.0 a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins 0.57 49.0 3.10e-01 100.0% 67.7%
3287751 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.57 43.0 3.14e-01 82.9% 35.1%
3582701 327.5.1.2 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 › AMP-binding_C 0.56 45.0 3.93e-01 88.6% 68.2%
3956317 2498.1.1.9 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M1 0.56 46.0 3.27e-01 100.0% 84.5%
2755357 232.1.1.3 a+b duplicates or obligate multimers › Pentein › Pentein › Pentein › PAD 0.56 43.0 2.84e-01 88.6% 41.2%
3960560 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 0.56 45.0 3.69e-01 88.6% 55.4%
3633853 300.1.1.3 a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › Tyr-DNA_phospho 0.55 38.0 2.61e-01 71.4% 75.9%
4125352 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 44.0 3.67e-01 88.6% 73.1%
4587994 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 0.54 42.0 3.57e-01 88.6% 70.8%
4622549 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 0.54 43.0 3.61e-01 88.6% 72.8%
4052385 2003.1.10.14 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain › Rimk_N 0.54 37.0 3.25e-01 71.4% 96.2%
3727070 206.1.1.15 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Fructosamin_kin 0.52 42.0 2.83e-01 87.1% 74.2%
3401452 2496.1.1.0 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like 0.52 45.0 3.64e-01 100.0% 90.0%
4065149 513.1.1.1 a+b two layers › Obg GTP-binding protein C-terminal domain-like › Obg GTP-binding protein C-terminal domain › Obg GTP-binding protein C-terminal domain › DUF1967 0.51 35.0 3.37e-01 70.0% 89.2%
2486980 221.16.1.1 a+b two layers › beta-Grasp › beta-grasp domain of MAJIN › beta-grasp domain of MAJIN › MAJIN 0.51 36.0 3.16e-01 72.9% 92.2%
3591078 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.51 42.0 4.27e-01 91.4% 100.0%
3190911 12.6.1.0 beta sandwiches › Glycosyl hydrolase domain-like › Glycoside hydrolase family 127 middle domain-related › Glycoside hydrolase family 127 middle domain-related 0.51 36.0 3.78e-01 74.3% 100.0%
3994433 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 0.51 40.0 3.75e-01 87.1% 71.1%
4021181 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 0.51 40.0 3.28e-01 88.6% 61.4%
11465 2496.1.1.4 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › SpoIIAA-like 0.51 40.0 3.49e-01 94.3% 96.8%
4175432 246.1.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.50 37.0 2.57e-01 82.9% 50.2%
4996359 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 0.50 40.0 3.51e-01 91.4% 67.8%
D3 medium residues 278-353
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 28.6 1.30e-06 100.0% 30.6%
D5 medium residues 533-653
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 52.3 5.70e-14 100.0% 30.7%
D6 medium residues 931-957_985-1020
PDB