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DNA_polymerase

Euk-Vir

Artogeia_rapae_granulovirus

DNA_polymerase__YP_003429417__Artogeia_rapae_granulovirus__362830

Identity

Accession:
YP_003429417 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

84.0 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Betabaculovirus› Betabaculovirus_arrapae

TaxID: 362830

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 53-201
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D2 medium residues 347-429
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009342373__Spheniscid_alphaherpesvirus_1__2560777__D504-588
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1d5aA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.88 80.0 5.73e-01 100.0% 37.3%
2gv9A03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.87 79.0 5.65e-01 98.8% 36.7%
4qclA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.84 78.0 5.24e-01 98.8% 42.4%
1s5jA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.82 72.0 5.33e-01 95.2% 39.7%
4fvmA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.79 73.0 5.16e-01 100.0% 38.0%
1noyB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.78 69.0 4.96e-01 100.0% 35.4%
2e6mA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.73 64.0 4.84e-01 94.0% 53.2%
6vddD01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 57.0 4.34e-01 98.8% 65.9%
3ungC04 1.20.120.1260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle 0.61 33.0 3.13e-01 71.1% 45.4%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.56 39.0 4.32e-01 73.5% 96.8%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.55 38.0 3.46e-01 88.0% 50.9%
2b5dX02 1.20.1430.10 Mainly Alpha › Up-down Bundle › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase, middle domain 0.51 39.0 3.59e-01 85.5% 63.2%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5035328 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.92 87.0 6.04e-01 100.0% 36.2%
5067181 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.92 87.0 5.33e-01 100.0% 21.0%
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 0.91 86.0 5.14e-01 100.0% 17.9%
5023018 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.90 80.0 5.76e-01 97.6% 37.1%
5029084 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.90 85.0 5.97e-01 100.0% 38.2%
4282509 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 82.0 4.83e-01 100.0% 14.3%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 85.0 4.86e-01 100.0% 12.3%
5081878 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 81.0 5.10e-01 100.0% 21.9%
5069333 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.89 81.0 5.04e-01 100.0% 21.1%
5054032 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.89 84.0 5.27e-01 100.0% 22.7%
5017082 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.89 80.0 5.11e-01 100.0% 22.5%
4452101 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 82.0 5.83e-01 100.0% 37.3%
None — 0.88 83.0 4.80e-01 100.0% 14.4%
3368695 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.88 83.0 5.18e-01 100.0% 23.6%
5025208 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.88 79.0 5.56e-01 100.0% 34.3%
4958553 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 79.0 5.62e-01 100.0% 35.9%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.88 82.0 5.32e-01 100.0% 26.9%
4502019 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 78.0 4.81e-01 100.0% 19.3%
3995965 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 79.0 5.91e-01 97.6% 46.5%
4981192 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.86 78.0 5.36e-01 100.0% 31.4%
4932453 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 5.25e-01 100.0% 36.9%
3825992 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 80.0 5.49e-01 100.0% 35.2%
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 0.85 79.0 4.56e-01 100.0% 13.3%
4023334 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 5.29e-01 100.0% 31.4%
3206356 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.85 79.0 4.91e-01 100.0% 22.0%
5040509 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 75.0 4.83e-01 100.0% 22.9%
3192875 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.84 77.0 4.67e-01 98.8% 17.2%
3784398 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 5.34e-01 100.0% 34.5%
4997716 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 76.0 5.43e-01 98.8% 53.3%
5051934 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 5.50e-01 100.0% 40.9%
4929239 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 5.03e-01 100.0% 27.4%
4002044 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 76.0 4.90e-01 98.8% 24.4%
4972218 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 76.0 4.58e-01 98.8% 17.2%
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 0.83 76.0 4.43e-01 100.0% 13.1%
3520437 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 75.0 5.54e-01 98.8% 42.1%
4218318 2484.1.1.295 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, RNase_H_2 0.82 76.0 4.95e-01 98.8% 26.9%
5076614 2484.1.1.328 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B 0.82 76.0 4.41e-01 98.8% 13.7%
4983222 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 76.0 4.80e-01 98.8% 23.9%
4874454 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.82 75.0 5.12e-01 98.8% 42.3%
3606428 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 75.0 5.31e-01 100.0% 37.9%
3794217 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.81 76.0 4.51e-01 100.0% 17.2%
3797773 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 76.0 5.03e-01 100.0% 30.8%
4934764 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 75.0 4.77e-01 98.8% 23.3%
4951831 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.81 73.0 4.81e-01 96.4% 60.7%
5027090 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 5.15e-01 98.8% 33.9%
3214818 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.80 73.0 4.65e-01 100.0% 22.1%
4029124 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.78 66.0 4.57e-01 100.0% 28.8%
11143 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 4.42e-01 100.0% 22.9%
4975018 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.72 64.0 4.81e-01 96.4% 43.1%
3750086 150.3.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.58 46.0 3.54e-01 88.0% 82.1%
3273431 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.57 42.0 3.83e-01 79.5% 65.2%
3635982 3567.1.1.141 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › DUF3435 0.55 38.0 3.93e-01 88.0% 75.0%
D3 medium residues 515-549_572-601
PDB
Domain cluster: rep: DNA_polymerase__YP_009316112__Anticarsia_gemmatalis_multiple_nucleopolyhedrovirus__268591__D473-499_523-556
D4 medium residues 550-571_639-784
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 70.4 1.90e-19 86.9% 30.0%