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DNA_polymerase

Euk-Vir

Bovine_gammaherpesvirus_6

DNA_polymerase__YP_009041990__Bovine_gammaherpesvirus_6__1504288

Identity

Accession:
YP_009041990 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

90.2 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Macavirus› Bovine_gammaherpesvirus_6

TaxID: 1504288

Cluster

View cluster (158 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 283-497
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 172.0 2.10e-50 77.2% 73.1%
D2 medium residues 86-281
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 36.9 3.90e-09 33.2% 24.4%
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA01 2.40.50.730 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.83 41.0 6.02e-01 99.5% 99.0%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 34.0 4.64e-01 86.2% 88.2%
1j2vA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 33.0 4.51e-01 74.5% 86.1%
3ahpA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 35.0 4.62e-01 87.2% 87.7%
4y6iA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 34.0 4.55e-01 86.2% 87.4%
2nuhA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 34.0 4.57e-01 86.2% 88.5%
4e98C00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 34.0 4.51e-01 86.2% 87.6%
4iyqA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 34.0 4.51e-01 83.7% 86.9%
2zomA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 34.0 4.51e-01 85.2% 88.8%
6gdxA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 35.0 4.53e-01 80.6% 89.7%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 31.0 4.42e-01 74.0% 98.9%
5d4nC00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 31.0 4.22e-01 80.6% 92.9%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.62 32.0 3.86e-01 77.6% 73.1%
2cz4A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 31.0 4.22e-01 79.6% 94.9%
4rx6D00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 33.0 4.39e-01 82.1% 96.3%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 30.0 4.29e-01 70.9% 100.0%
2yq1C00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.60 33.0 3.89e-01 86.7% 77.1%
2jdjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 30.0 4.06e-01 75.0% 96.2%
1rjjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 32.0 4.16e-01 89.3% 96.4%
3bdeB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 30.0 4.10e-01 74.0% 100.0%
1tr0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 32.0 4.19e-01 82.7% 100.0%
2fiuA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 29.0 4.00e-01 75.5% 100.0%
1xjvA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 35.0 4.12e-01 100.0% 85.9%
3bguA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 29.0 3.97e-01 75.0% 100.0%
5xzqF00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 30.0 4.07e-01 76.0% 100.0%
1mwqA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.55 30.0 3.97e-01 86.2% 100.0%
1rtzA00 3.30.70.560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK 0.50 35.0 3.86e-01 78.6% 89.5%
4fprB00 3.30.70.2910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 31.0 3.73e-01 85.7% 93.0%
3ramA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 30.0 3.85e-01 82.1% 100.0%
3jvaA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 28.0 3.62e-01 92.9% 93.9%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4997715 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.89 75.0 8.02e-01 99.5% 99.4%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.88 76.0 5.02e-01 100.0% 25.8%
3704723 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.88 50.0 6.32e-01 99.5% 89.6%
3592676 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.87 50.0 6.30e-01 99.5% 89.6%
3501565 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.87 63.0 7.36e-01 97.4% 100.0%
3350050 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.87 50.0 5.87e-01 100.0% 77.9%
4500300 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 69.0 5.38e-01 97.4% 42.1%
4942684 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.86 72.0 7.68e-01 98.0% 99.4%
4944520 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.84 73.0 6.88e-01 96.4% 76.5%
3932593 2.1.1.179 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › REV3_N 0.83 45.0 6.22e-01 95.4% 100.0%
4299557 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.83 70.0 7.03e-01 97.4% 87.2%
3788812 304.114.1.6 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › DNA_pol_B_exo1 0.82 75.0 6.94e-01 99.0% 77.1%
5023017 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.82 67.0 6.47e-01 97.4% 76.3%
3800859 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.82 74.0 7.43e-01 94.4% 100.0%
3794217 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.81 76.0 5.38e-01 98.0% 53.2%
5048995 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 68.0 5.30e-01 99.5% 45.6%
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 0.80 75.0 4.89e-01 100.0% 26.3%
3192875 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.78 74.0 5.38e-01 99.5% 47.8%
3741555 4969.1.1.0 ↗ alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.77 59.0 5.56e-01 79.1% 77.8%
3266685 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.76 69.0 4.11e-01 100.0% 16.0%
3166912 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.75 54.0 5.52e-01 73.5% 94.7%
3705696 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.74 69.0 6.49e-01 99.5% 83.5%
3605750 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.73 70.0 4.39e-01 100.0% 21.8%
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 0.73 70.0 4.39e-01 100.0% 23.3%
4448420 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.72 68.0 6.28e-01 99.5% 80.4%
4945381 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.71 32.0 4.89e-01 77.6% 100.0%
4405678 304.114.1.6 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › DNA_pol_B_exo1 0.71 67.0 5.96e-01 98.5% 79.2%
4937786 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.70 34.0 4.63e-01 86.2% 89.0%
4803119 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.70 34.0 4.55e-01 85.7% 85.6%
4944847 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.70 35.0 4.63e-01 87.2% 87.5%
4629521 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.70 34.0 4.59e-01 85.7% 86.5%
5038160 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.70 34.0 4.65e-01 86.7% 90.0%
4957224 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 34.0 4.62e-01 86.2% 90.0%
4140821 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 34.0 4.55e-01 86.7% 86.7%
5000967 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 34.0 4.57e-01 81.1% 87.6%
222842 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 34.0 4.50e-01 85.7% 85.8%
5015958 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 34.0 4.52e-01 86.2% 87.5%
3583468 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.69 36.0 4.71e-01 89.3% 90.0%
3459357 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.68 35.0 4.40e-01 83.7% 81.7%
4928840 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.68 33.0 4.48e-01 85.7% 89.0%
2485059 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.66 36.0 4.57e-01 82.7% 89.3%
5037829 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.66 33.0 4.48e-01 86.2% 92.0%
3648704 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.66 32.0 4.52e-01 86.2% 98.9%
3823137 304.126.1.1 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.64 34.0 3.92e-01 87.2% 69.3%
3555669 304.126.1.1 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.64 32.0 3.96e-01 87.2% 75.8%
402134 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.63 35.0 4.42e-01 82.1% 89.0%
3417210 304.126.1.1 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.63 31.0 4.33e-01 83.7% 100.0%
5076410 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.62 57.0 4.46e-01 94.4% 88.4%
1721576 304.5.1.1 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.62 34.0 4.48e-01 85.7% 96.3%
4982659 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 54.0 4.37e-01 94.4% 92.3%
4656922 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 32.0 3.91e-01 90.3% 84.2%
4428345 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.58 32.0 3.13e-01 90.8% 47.4%
3483966 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.58 31.0 4.07e-01 78.6% 95.2%
3579336 304.5.1.23 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › V_ATPase_I 0.57 33.0 4.24e-01 80.1% 100.0%
3168849 304.114.1.2 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › POL3_N 0.55 40.0 4.65e-01 85.7% 100.0%
4261090 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.55 29.0 2.80e-01 83.2% 41.3%
4463387 304.5.1.18 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › PrmA 0.55 29.0 3.89e-01 76.0% 95.2%
3280665 304.4.1.10 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF1330 0.55 32.0 4.07e-01 80.1% 100.0%
3367463 304.4.1.14 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dabb 0.55 32.0 4.06e-01 92.3% 100.0%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.54 48.0 3.94e-01 92.3% 96.2%
3782802 304.15.1.0 ↗ a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain 0.54 34.0 3.53e-01 75.0% 67.8%
3283902 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.53 33.0 2.98e-01 91.8% 43.7%
D3 medium residues 549-573_715-812
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_002608259__Human_herpesvirus_5__10359__D703-718_902-984
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 98.6 5.10e-28 79.7% 19.0%
PF00136.27 DNA_pol_B 23.2 3.80e-05 23.6% 5.3%
D4 medium residues 574-628_662-714
PDB
Domain cluster: rep: rh87__YP_068180__Macacine_betaherpesvirus_3__47929__D595-644_698-744
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 54.4 1.30e-14 51.8% 11.7%
PF00136.27 DNA_pol_B 82.0 5.60e-23 50.9% 11.3%
D5 medium residues 813-993
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__NP_073324__Meleagrid_alphaherpesvirus_1__37108__D926-999_1042-1063_1105-1149
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 135.5 3.40e-39 91.7% 33.3%