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DNA_polymerase

Euk-Vir

BeAn_58058_virus

DNA_polymerase__YP_009329664__BeAn_58058_virus__67082

Identity

Accession:
YP_009329664 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

84.4 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Oryzopoxvirus› BeAn_58058_virus

TaxID: 67082

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 161-343
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_401712__Human_gammaherpesvirus_4__10376__D288-457
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 77.7 1.30e-21 100.0% 69.8%
D2 high residues 830-998
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 108.4 5.80e-31 93.5% 32.9%
D3 medium residues 2-156
PDB
Domain cluster: rep: DNA_polymerase__YP_784249__Nile_crocodilepox_virus__1285600__D2-148
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08452.17 best DNAP_B_exo_N 49.6 2.70e-13 13.6% 95.5%
D4 medium residues 346-433
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 75.0 9.00e-21 96.6% 62.5%
D5 medium residues 531-554_747-829
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 88.7 5.50e-25 78.5% 17.7%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qexA03 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.87 81.0 6.04e-01 99.1% 95.9%
1q8iA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.85 81.0 6.26e-01 100.0% 74.6%
4fxdA05 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.83 76.0 7.40e-01 97.2% 95.7%
2gv9B04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.83 76.0 6.06e-01 97.2% 99.5%
2py5A02 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.73 69.0 5.68e-01 100.0% 78.2%
1tdqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 37.0 3.91e-01 76.6% 62.8%
2govA01 3.20.80.10 Alpha Beta › Alpha-Beta Barrel › Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A › Regulatory factor, effector binding domain 0.60 42.0 3.62e-01 72.9% 88.4%
2dliA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 36.0 3.79e-01 75.7% 64.3%
4wtxA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 35.0 3.72e-01 76.6% 62.9%
4z9mB02 3.30.590.10 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › Glutamine synthetase/guanido kinase, catalytic domain 0.60 46.0 3.78e-01 82.2% 96.0%
6wl5A01 3.20.80.10 Alpha Beta › Alpha-Beta Barrel › Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A › Regulatory factor, effector binding domain 0.60 41.0 3.73e-01 71.0% 96.0%
1mfnA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 35.0 3.68e-01 75.7% 65.6%
6gbuD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.57 30.0 3.76e-01 88.8% 85.9%
3qt2A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 31.0 3.25e-01 76.6% 56.7%
2qggA02 2.30.30.240 Mainly Beta › Roll › SH3 type barrels. › PRC-barrel domain 0.55 32.0 3.56e-01 95.3% 72.3%
5cw3C01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 49.0 4.40e-01 99.1% 95.9%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 46.0 4.17e-01 96.3% 96.1%
4i9xA00 2.60.40.3790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 43.0 3.54e-01 86.9% 67.4%
6qe7A01 3.90.182.10 Alpha Beta › Alpha-Beta Complex › Toxin - Anthrax Protective Antigen; domain 1 › Toxin - Anthrax Protective Antigen;domain 1 0.51 36.0 3.36e-01 78.5% 58.1%
3o4lD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 34.0 3.53e-01 75.7% 72.1%
4geiA00 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 37.0 3.38e-01 76.6% 70.8%
7mxdX01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 36.0 3.55e-01 76.6% 74.8%
3bgaA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 33.0 3.31e-01 76.6% 64.9%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3089539 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 0.95 79.0 5.52e-01 86.0% 97.6%
4029141 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 0.91 88.0 6.32e-01 100.0% 92.3%
4231530 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 0.91 87.0 6.76e-01 100.0% 98.5%
3558196 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 0.91 87.0 6.10e-01 100.0% 86.7%
3615419 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 0.90 86.0 5.84e-01 100.0% 86.7%
3784383 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 0.90 85.0 5.63e-01 99.1% 70.5%
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 0.90 86.0 5.11e-01 100.0% 41.5%
None — 0.90 86.0 5.12e-01 100.0% 38.9%
3484036 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 0.90 84.0 6.00e-01 98.1% 98.5%
3684974 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 0.90 85.0 5.04e-01 99.1% 39.1%
None — 0.90 84.0 5.01e-01 98.1% 38.1%
3628202 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 0.90 86.0 5.07e-01 100.0% 37.3%
4022366 2484.1.1.161 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 85.0 5.06e-01 99.1% 38.7%
3993981 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 0.90 84.0 6.36e-01 98.1% 98.7%
3480546 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 0.90 86.0 6.15e-01 100.0% 97.7%
3597965 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 0.90 85.0 6.24e-01 99.1% 98.8%
3801150 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 0.90 85.0 5.96e-01 100.0% 82.0%
3466667 2484.1.1.161 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.88 83.0 4.96e-01 100.0% 34.2%
4276636 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 0.87 83.0 5.64e-01 100.0% 76.7%
5019480 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 0.87 83.0 4.84e-01 100.0% 36.1%
4629010 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.87 70.0 5.34e-01 84.1% 83.6%
3349591 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 0.86 81.0 5.73e-01 99.1% 79.0%
5005286 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 0.86 80.0 5.58e-01 98.1% 87.9%
3705695 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.86 79.0 5.87e-01 97.2% 86.1%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.86 82.0 4.85e-01 100.0% 34.1%
4144335 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.86 69.0 5.08e-01 85.0% 84.2%
3381141 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.85 67.0 5.62e-01 82.2% 94.1%
4944522 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 0.85 80.0 5.88e-01 98.1% 96.3%
3741560 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.85 79.0 5.75e-01 100.0% 83.7%
3206807 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.84 75.0 5.40e-01 93.5% 80.7%
4022145 2484.1.1.153 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1744 0.84 74.0 4.46e-01 92.5% 34.5%
4182409 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.84 73.0 6.31e-01 92.5% 93.1%
3189629 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 0.84 76.0 4.79e-01 96.3% 49.7%
4997717 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 5.45e-01 99.1% 85.8%
3266689 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.83 65.0 4.80e-01 82.2% 83.8%
3508610 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.83 64.0 4.72e-01 80.4% 82.7%
4958554 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 0.81 77.0 5.77e-01 100.0% 96.6%
3924217 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.81 62.0 4.59e-01 80.4% 83.1%
3464384 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.80 69.0 5.10e-01 91.6% 83.1%
4282509 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.79 74.0 4.52e-01 100.0% 31.5%
3797416 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 0.79 70.0 5.12e-01 95.3% 84.1%
3831499 304.48.1.63 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B, DUF1744 0.79 71.0 4.19e-01 96.3% 30.1%
5017083 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 0.79 73.0 5.29e-01 99.1% 85.6%
3474156 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.79 67.0 4.90e-01 91.6% 82.5%
3578106 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.78 73.0 5.27e-01 100.0% 83.3%
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 0.74 69.0 4.36e-01 99.1% 45.4%
3877126 304.48.1.24 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DUF1744 0.74 68.0 4.10e-01 100.0% 54.5%
4100823 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.72 65.0 4.95e-01 100.0% 84.0%
3506687 304.48.1.17 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.72 68.0 4.38e-01 100.0% 70.5%
3414433 304.4.1.52 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF7153 0.61 51.0 3.83e-01 90.7% 76.7%
4982678 11.1.1.103 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CARDB 0.57 34.0 3.51e-01 76.6% 60.0%
5079339 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.57 43.0 3.91e-01 78.5% 95.7%
3266198 6109.1.1.1 ↗ a+b two layers › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 › ChAPs 0.57 49.0 4.17e-01 96.3% 70.6%
3968511 304.45.1.1 ↗ a+b two layers › Alpha-beta plaits › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › HPPK 0.56 46.0 3.93e-01 89.7% 80.6%
3790957 3562.1.1.21 ↗ alpha bundles › Calcium release-activated calcium channel protein 1 › Calcium release-activated calcium channel protein 1 › Calcium release-activated calcium channel protein 1 › NRF 0.55 48.0 4.02e-01 95.3% 61.7%
3838981 4114.1.1.1 ↗ a+b two layers › PHP14-like › PHP14-like › PHP14-like › PP_kinase 0.54 49.0 3.97e-01 100.0% 69.8%
3928344 11.1.1.959 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ILCR1_N 0.52 41.0 3.63e-01 84.1% 87.7%
3270508 206.1.3.23 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RNA_ligase 0.52 38.0 3.01e-01 76.6% 78.6%
3910715 10.10.1.0 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) 0.52 40.0 3.72e-01 83.2% 100.0%
1698226 206.1.3.23 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RNA_ligase 0.51 37.0 3.02e-01 75.7% 81.4%