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DNA_polymerase

Euk-Vir

Pseudalatia_unipuncta_granulovirus

DNA_polymerase__YP_003422477__Pseudalatia_unipuncta_granulovirus__36355

Identity

Accession:
YP_003422477 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

81.7 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Betabaculovirus› Pseudalatia_unipuncta_granulovirus

TaxID: 36355

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 39-203
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D2 high residues 207-431
PDB
Domain cluster: rep: DNA_polymerase__YP_009118564__Condylorrhiza_vestigialis_MNPV__1592576__D196-404
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF10108.16 best DNA_pol_B_exo2 43.4 4.60e-11 88.0% 61.3%
PF03104.26 DNA_pol_B_exo1 86.3 3.20e-24 79.1% 73.1%
PF13482.13 RNase_H_2 25.2 2.00e-05 75.1% 72.1%
D3 medium residues 476-493_512-675
PDB
Domain cluster: rep: DNA_polymerase__YP_010086932__Cryptophlebia_peltastica_nucleopolyhedrovirus__2304025__D494-537_560-649
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 59.8 3.10e-16 86.8% 33.6%
D4 medium residues 676-752
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 25.9 6.00e-06 85.7% 9.5%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rwuA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.71 54.0 5.20e-01 100.0% 72.4%
4djbA00 3.30.70.2870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Mastadenovirus E4 ORF3 0.70 62.0 5.40e-01 100.0% 69.5%
5u89A01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.64 45.0 4.32e-01 100.0% 63.0%
4oycB00 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.64 54.0 5.15e-01 100.0% 82.0%
2kz0A01 3.30.300.90 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › BolA-like 0.63 47.0 4.82e-01 100.0% 87.3%
1vehA01 3.30.300.130 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Fe-S cluster assembly (FSCA) 0.61 47.0 4.75e-01 100.0% 86.7%
7lscA01 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.61 49.0 4.00e-01 89.6% 97.3%
1nnnA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.61 52.0 4.51e-01 100.0% 62.0%
6h1bA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.60 51.0 4.66e-01 100.0% 70.6%
8affD01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.60 50.0 5.03e-01 100.0% 92.3%
5uptA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.60 49.0 4.49e-01 100.0% 67.3%
3nyqA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.59 49.0 4.81e-01 100.0% 84.9%
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 37.0 3.58e-01 83.1% 53.3%
6ijbA01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.59 49.0 4.54e-01 100.0% 73.5%
3tviA02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.59 42.0 3.44e-01 100.0% 37.7%
2le1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.58 49.0 4.09e-01 100.0% 91.4%
2wssA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.58 36.0 3.42e-01 79.2% 50.5%
4isbB02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.58 50.0 4.57e-01 100.0% 72.0%
3eeaA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.58 48.0 3.92e-01 93.5% 94.8%
1cksB00 3.30.170.10 Alpha Beta › 2-Layer Sandwich › Cyclin-Dependent Kinase Subunit Type 2 › Cyclin-dependent kinase, regulatory subunit 0.58 39.0 3.92e-01 76.6% 67.9%
3dbaA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.57 48.0 3.75e-01 93.5% 88.3%
2jvrA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 41.0 4.08e-01 97.4% 75.0%
1haeA00 2.10.25.10 Mainly Beta › Ribbon › Laminin › Laminin 0.55 31.0 3.35e-01 70.1% 63.5%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 44.0 3.35e-01 92.2% 56.2%
2o5aA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 42.0 3.93e-01 100.0% 64.7%
6le1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 40.0 4.16e-01 87.0% 91.2%
4k59A00 2.60.40.4380 Mainly Beta › Sandwich › Immunoglobulin-like › Translational regulator CsrA 0.54 34.0 3.72e-01 83.1% 75.8%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.54 45.0 4.36e-01 96.1% 88.8%
7uclA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 40.0 3.73e-01 81.8% 63.7%
1hp7A01 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.53 42.0 4.00e-01 88.3% 90.5%
2op5B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 42.0 4.02e-01 100.0% 74.0%
1nz8A00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.52 45.0 3.99e-01 100.0% 67.2%
2zy2A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 43.0 3.52e-01 94.8% 47.7%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.51 42.0 3.09e-01 92.2% 90.4%
8d8lE01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 40.0 3.93e-01 90.9% 91.9%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4973750 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.75 55.0 5.62e-01 100.0% 80.8%
4982759 327.18.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › 40S ribosomal protein S7-A › 40S ribosomal protein S7-A 0.73 54.0 5.73e-01 97.4% 93.8%
3799886 304.8.1.49 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › R1_ABCA1 0.70 49.0 5.17e-01 100.0% 81.4%
5019384 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.68 56.0 5.23e-01 100.0% 73.7%
2495100 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 0.65 55.0 4.49e-01 100.0% 50.7%
4130841 304.28.1.2 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.63 48.0 4.60e-01 100.0% 71.1%
5036264 304.39.1.1 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain › MS_channel_3rd 0.63 54.0 4.96e-01 100.0% 72.4%
4556741 309.1.1.11 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › PqqF-like_C_4 0.63 55.0 4.30e-01 100.0% 72.0%
4943823 304.162.1.0 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.62 49.0 4.92e-01 97.4% 85.0%
1125575 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.61 51.0 4.03e-01 93.5% 89.1%
3617823 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.61 47.0 4.46e-01 93.5% 69.9%
4799073 309.1.1.4 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C 0.61 48.0 4.47e-01 89.6% 68.4%
3962577 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 4.94e-01 87.0% 95.7%
5053617 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 50.0 4.56e-01 100.0% 67.6%
4388283 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.60 45.0 4.64e-01 100.0% 88.6%
5001360 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.60 47.0 3.07e-01 88.3% 20.0%
3744741 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 50.0 4.61e-01 100.0% 72.0%
3483105 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.60 46.0 4.19e-01 89.6% 60.0%
3957699 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 45.0 4.50e-01 100.0% 78.8%
4602065 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 0.59 48.0 4.27e-01 100.0% 60.9%
3650594 304.8.1.47 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_ACR9_3rd 0.59 49.0 3.80e-01 100.0% 40.0%
4886051 304.8.1.8 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_4 0.59 44.0 4.36e-01 100.0% 78.8%
5886 327.2.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › BolA-like › BolA-like › BolA 0.59 47.0 4.25e-01 100.0% 61.9%
3992245 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.59 46.0 4.66e-01 100.0% 89.3%
5073850 304.43.1.6 ↗ a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 › FLAD1_M 0.59 45.0 4.59e-01 83.1% 85.3%
3482558 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.58 49.0 4.78e-01 94.8% 88.2%
3970968 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 0.58 49.0 4.45e-01 100.0% 68.2%
3705453 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.58 49.0 3.55e-01 100.0% 60.8%
3467262 1.1.11.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain 0.58 37.0 3.06e-01 75.3% 34.5%
3959346 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 0.57 50.0 4.32e-01 100.0% 88.0%
3363114 325.1.7.25 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › PORR 0.57 32.0 3.09e-01 100.0% 46.7%
3684154 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 48.0 4.81e-01 98.7% 96.2%
3957515 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 46.0 4.14e-01 100.0% 63.5%
4957785 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.56 45.0 4.11e-01 92.2% 80.0%
1211453 2498.1.1.23 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M49 0.55 47.0 2.78e-01 100.0% 30.5%
5065308 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.55 38.0 3.32e-01 72.7% 95.0%
4963939 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.54 38.0 3.99e-01 93.5% 87.7%
3446538 5061.1.1.1 ↗ alpha complex topology › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › SecY 0.54 42.0 2.66e-01 87.0% 22.0%
1224463 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.53 32.0 3.75e-01 70.1% 93.9%
3657148 305.1.1.2 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L_2 0.53 36.0 3.78e-01 79.2% 78.6%
3587631 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.52 45.0 3.77e-01 100.0% 81.4%
3685475 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.52 43.0 4.28e-01 100.0% 93.8%
3853169 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.51 42.0 2.74e-01 89.6% 38.0%
3180028 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.51 41.0 2.68e-01 88.3% 77.0%
1834407 3218.1.1.1 ↗ a+b duplicates or obligate multimers › small terminase oligomerization domain › small terminase oligomerization domain › small terminase oligomerization domain › Terminase_2 0.51 35.0 3.51e-01 93.5% 69.2%
5040059 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 39.0 3.41e-01 81.8% 96.5%
3627409 6166.1.1.1 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › ERG4_ERG24 0.51 42.0 3.18e-01 94.8% 74.5%
4994432 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 34.0 3.09e-01 87.0% 50.5%