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DNA_polymerase

Euk-Vir

Lonomia_obliqua_multiple_nucleopolyhedrovirus

DNA_polymerase__YP_009666438__Lonomia_obliqua_multiple_nucleopolyhedrovirus__134394

Identity

Accession:
YP_009666438 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

83.5 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Lonomia_obliqua_multiple_nucleopolyhedrovirus

TaxID: 134394

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 190-431
PDB
Domain cluster: rep: DNA_polymerase__YP_009118564__Condylorrhiza_vestigialis_MNPV__1592576__D196-404
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF10108.16 best DNA_pol_B_exo2 37.1 3.70e-09 73.6% 67.0%
PF03104.26 DNA_pol_B_exo1 82.4 4.80e-23 72.7% 73.6%
D2 medium residues 21-187
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D3 medium residues 467-516_540-629
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 27.0 2.90e-06 65.7% 12.8%
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.80 36.0 5.61e-01 82.9% 100.0%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 30.0 4.66e-01 92.1% 83.6%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.76 32.0 4.92e-01 97.9% 93.4%
1u5eA01 6.10.250.220 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.74 30.0 4.78e-01 99.3% 100.0%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 36.0 4.97e-01 79.3% 91.8%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.72 36.0 4.44e-01 100.0% 75.0%
2p4vA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.71 37.0 4.98e-01 97.1% 93.4%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 34.0 4.57e-01 97.9% 91.5%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 33.0 4.71e-01 77.9% 100.0%
7k18A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.68 36.0 3.77e-01 95.7% 53.7%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.68 31.0 3.64e-01 100.0% 58.8%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 32.0 4.32e-01 75.7% 85.1%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.67 37.0 4.38e-01 77.1% 76.8%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.67 34.0 4.44e-01 80.0% 86.3%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.66 32.0 4.48e-01 80.0% 100.0%
1vctA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.65 36.0 4.02e-01 99.3% 67.9%
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.64 36.0 4.64e-01 72.1% 94.0%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.63 36.0 4.33e-01 92.9% 88.4%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.62 33.0 4.17e-01 72.9% 89.7%
3axjB01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.61 35.0 3.39e-01 78.6% 49.0%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.58 25.0 3.54e-01 97.9% 83.6%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 38.0 4.07e-01 100.0% 77.5%
3purA03 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 30.0 3.37e-01 99.3% 66.4%
4dyqA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.51 33.0 3.83e-01 95.7% 88.3%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.51 34.0 3.42e-01 100.0% 65.5%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4213046 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.83 39.0 5.83e-01 96.4% 100.0%
4883924 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.76 39.0 5.17e-01 82.1% 88.7%
3742811 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.76 39.0 4.32e-01 98.6% 61.7%
3505608 192.29.1.1 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB_dom 0.72 39.0 5.31e-01 82.1% 100.0%
4972401 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.72 41.0 3.51e-01 87.1% 36.7%
5082565 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.71 35.0 4.91e-01 76.4% 95.7%
4998819 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.71 40.0 4.17e-01 86.4% 59.2%
3971539 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.70 38.0 5.07e-01 88.6% 98.7%
4999065 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.70 40.0 3.86e-01 70.0% 50.3%
5017725 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.70 40.0 3.55e-01 87.1% 40.5%
3253283 192.5.1.14 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.70 42.0 4.99e-01 99.3% 87.4%
3755476 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.69 38.0 3.50e-01 79.3% 42.9%
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 0.68 57.0 4.39e-01 85.7% 57.5%
4996586 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.68 37.0 3.79e-01 85.7% 53.6%
3956669 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.68 41.0 3.75e-01 86.4% 46.7%
3299091 3567.1.1.126 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › PF29520 0.67 37.0 3.84e-01 82.9% 55.6%
4977429 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.66 38.0 3.86e-01 87.1% 56.4%
3955489 2484.1.1.211 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605, Cas12f1-like_TNB 0.66 43.0 3.72e-01 90.0% 43.8%
3642421 603.1.1.5 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin-6_N 0.66 40.0 4.25e-01 100.0% 68.0%
5005094 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.65 39.0 3.44e-01 87.1% 42.1%
None — 0.65 62.0 3.87e-01 100.0% 23.3%
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 0.64 57.0 4.50e-01 92.9% 57.0%
3286637 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.64 37.0 3.53e-01 86.4% 47.3%
4977369 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 0.64 61.0 4.88e-01 100.0% 56.4%
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 0.64 61.0 4.68e-01 100.0% 51.6%
4970593 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 0.64 61.0 4.86e-01 100.0% 56.8%
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 0.63 60.0 4.53e-01 100.0% 48.2%
4956224 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 0.63 60.0 4.95e-01 100.0% 60.0%
4959101 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 0.63 59.0 4.74e-01 97.9% 59.6%
4000107 3567.1.1.122 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › BAR 0.63 35.0 3.40e-01 82.9% 48.1%
4982660 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 0.62 54.0 4.57e-01 97.9% 58.6%
4977784 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.62 38.0 3.22e-01 87.1% 36.2%
3582116 1147.1.1.1 ↗ alpha bundles › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › Occludin_ELL 0.62 34.0 3.70e-01 76.4% 61.7%
4774281 1147.1.1.1 ↗ alpha bundles › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › Occludin_ELL 0.62 37.0 4.20e-01 77.1% 77.1%
3622615 604.1.1.172 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › 7TM_GPCR_Srx 0.61 35.0 3.99e-01 100.0% 74.3%
4864755 5001.1.1.6 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Bac_rhodopsin 0.61 44.0 3.71e-01 72.9% 52.3%
5073476 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 0.60 54.0 4.41e-01 97.1% 55.3%
3271963 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.59 41.0 3.90e-01 98.6% 60.0%
5012084 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 0.59 54.0 4.51e-01 98.6% 60.0%
5044377 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 0.58 53.0 4.36e-01 97.9% 58.4%
5040510 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 0.58 51.0 4.17e-01 93.6% 61.2%
4947400 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.57 43.0 4.38e-01 100.0% 78.6%
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 0.56 50.0 3.90e-01 100.0% 50.0%
3366776 109.4.1.1690 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_17, TPR_16 0.56 29.0 2.57e-01 76.4% 32.1%
4259997 192.15.1.133 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › NST1 0.55 30.0 3.40e-01 77.9% 66.4%
3779105 3602.1.1.16 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › SHCBP_N 0.55 40.0 3.87e-01 73.6% 100.0%
3588519 101.1.2.49 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.55 32.0 3.08e-01 100.0% 46.1%
4952853 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.55 30.0 3.57e-01 77.1% 76.8%
3229891 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.54 41.0 4.16e-01 77.1% 94.8%
4003906 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.53 37.0 3.83e-01 70.7% 95.4%
3192393 2004.1.1.430 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, ABC_tran_Xtn 0.52 47.0 3.08e-01 100.0% 26.2%
4581983 5086.1.1.13 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › T3SSipB 0.51 38.0 3.81e-01 77.9% 76.4%
5005799 5069.1.1.15 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.50 37.0 3.26e-01 76.4% 67.1%
D4 medium residues 630-722
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009552191__Malacosoma_neustria_nucleopolyhedrovirus__38012__D557-567_668-765
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 40.3 2.60e-10 100.0% 20.8%
D5 medium residues 754-818_838-949_988-1001
PDB
Domain cluster: rep: hypothetical_protein_MIV120R__YP_654692__Invertebrate_iridescent_virus_3__345201__D821-880_935-1042