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DNA_polymerase

Euk-Vir

Mythimna_separata_entomopoxvirus_L

DNA_polymerase__YP_008003592__Mythimna_separata_entomopoxvirus_L__1293572

Identity

Accession:
YP_008003592 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

71.1 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Betaentomopoxvirus› Mythimna_separata_entomopoxvirus_'L'

TaxID: 1293572

Cluster

View cluster (158 members)

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 425-525
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_009162448__Salmon_gill_poxvirus__1680908__D388-474
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08408.17 best DNA_pol_B_3 35.3 1.70e-08 95.0% 72.7%
D2 high residues 927-1104
PDB
Domain cluster: rep: IMGVR_UViG_3300021255_003095-3300021255-Ga0223825_1010595139__D209-342
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 30.4 2.60e-07 93.3% 32.9%
D3 medium residues 42-115_159-173_185-243
PDB
D4 medium residues 244-348
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_010088005__Lymphocystis_disease_virus_4__2704413__D159-241
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 52.0 9.00e-14 99.1% 40.9%
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3f2bA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.68 35.0 3.62e-01 98.1% 52.1%
2a1rB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 51.0 3.67e-01 98.1% 46.9%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.57 47.0 3.53e-01 90.5% 76.5%
3bjsA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 33.0 3.23e-01 97.1% 51.3%
2oc3A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.56 45.0 3.42e-01 90.5% 77.8%
1yguA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.56 45.0 3.41e-01 90.5% 75.4%
1b78A00 3.90.950.10 Alpha Beta › Alpha-Beta Complex › Maf protein › 0.55 39.0 3.32e-01 74.3% 66.8%
4qunA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.54 48.0 3.56e-01 100.0% 88.3%
2xxpA02 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.54 42.0 3.15e-01 100.0% 32.7%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.53 33.0 3.43e-01 95.2% 64.7%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 35.0 3.33e-01 98.1% 55.9%
3qcmA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.53 45.0 3.40e-01 98.1% 88.1%
4qozB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 46.0 3.70e-01 100.0% 85.6%
3l1wA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.51 36.0 2.81e-01 74.3% 68.5%
1hqz800 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.51 35.0 3.32e-01 72.4% 82.6%
4depC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 31.0 3.19e-01 83.8% 63.7%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4492006 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 52.0 3.73e-01 100.0% 23.7%
4990754 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 54.0 4.05e-01 100.0% 29.8%
5039400 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 54.0 3.75e-01 100.0% 22.7%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 54.0 3.70e-01 100.0% 21.6%
4939488 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 54.0 3.84e-01 100.0% 24.1%
5036329 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 50.0 3.72e-01 100.0% 26.8%
5027238 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.82 47.0 4.14e-01 98.1% 40.7%
5043498 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.80 53.0 3.49e-01 100.0% 18.2%
3089543 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 71.0 5.50e-01 97.1% 46.9%
4957483 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.78 53.0 4.23e-01 98.1% 37.0%
5029084 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.77 56.0 4.26e-01 100.0% 35.1%
None — 0.76 60.0 4.01e-01 99.0% 23.6%
3710418 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.76 60.0 3.97e-01 99.0% 22.9%
3825992 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 61.0 4.55e-01 100.0% 36.8%
3606428 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.71 60.0 4.53e-01 98.1% 40.0%
3496492 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.70 65.0 4.62e-01 100.0% 38.6%
3705562 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.69 58.0 3.46e-01 99.0% 14.0%
3797773 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.68 59.0 4.16e-01 100.0% 32.5%
3994653 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 46.0 3.73e-01 98.1% 38.4%
3590721 2484.1.1.86 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TerL_nuclease 0.58 45.0 3.63e-01 99.0% 41.9%
3587035 2484.1.1.86 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TerL_nuclease 0.57 46.0 3.68e-01 100.0% 42.9%
3927145 2007.2.3.21 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase, PTP-SAK 0.57 43.0 3.15e-01 81.9% 71.8%
3396462 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.56 33.0 4.06e-01 95.2% 93.8%
3803681 2484.1.1.45 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › CAF1 0.55 50.0 3.52e-01 98.1% 46.7%
2494924 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.55 32.0 3.61e-01 95.2% 76.9%
3666591 2484.1.1.36 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.54 43.0 3.27e-01 100.0% 36.4%
3914493 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 46.0 2.91e-01 98.1% 44.7%
3867704 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 46.0 3.36e-01 98.1% 82.9%
3993235 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.53 47.0 3.78e-01 100.0% 93.5%
4966854 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 50.0 3.33e-01 100.0% 48.6%
4997175 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.53 33.0 3.28e-01 98.1% 59.1%
3598159 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.53 37.0 3.53e-01 73.3% 88.4%
4018340 246.3.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos 0.52 36.0 2.99e-01 72.4% 85.7%
3740496 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.52 38.0 3.51e-01 75.2% 86.9%
3517413 2007.2.3.21 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase, PTP-SAK 0.52 45.0 3.33e-01 99.0% 87.5%
4404889 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 39.0 3.16e-01 78.1% 75.4%
5006387 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 39.0 3.30e-01 78.1% 74.7%
6800 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.51 37.0 3.38e-01 74.3% 82.0%
3691964 206.1.1.82 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › DUF7580 0.51 42.0 2.98e-01 93.3% 50.4%
174115 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.51 27.0 2.95e-01 91.4% 60.0%
3969050 231.1.1.3 ↗ a+b two layers › MocoBD/DmpA-related › MocoBD/DmpA-related › Molybdenum cofactor-binding domain › MoCoBD_1, MoCoBD_2 0.51 45.0 2.85e-01 100.0% 68.4%
3543955 378.1.1.1 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › Endonuclease_NS 0.50 39.0 2.82e-01 80.0% 37.0%
3255601 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.50 43.0 4.06e-01 93.3% 84.0%
D5 medium residues 625-654_780-926
PDB
Domain cluster: rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 64.6 1.10e-17 85.9% 26.5%