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DNA_polymerase

Euk-Vir

Spodoptera_exempta_nucleopolyhedrovirus

DNA_polymerase__YP_010086507__Spodoptera_exempta_nucleopolyhedrovirus__1242863

Identity

Accession:
YP_010086507 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

82.1 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Spodoptera_exempta_nucleopolyhedrovirus

TaxID: 1242863

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 medium residues 193-331
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 72.3 5.90e-20 97.1% 50.8%
D2 medium residues 332-432
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009342373__Spheniscid_alphaherpesvirus_1__2560777__D504-588
D3 medium residues 433-497_594-647
PDB
Domain cluster: rep: IMGVR_UViG_3300048031_000811-3300048031-Ga0494182_008429_2395_4416__D190-244_288-384
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 35.5 7.40e-09 86.6% 12.6%
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 39.0 5.49e-01 94.1% 98.4%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.74 40.0 4.99e-01 95.8% 85.3%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.73 41.0 3.84e-01 95.8% 45.8%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.72 40.0 5.03e-01 95.0% 87.8%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.71 40.0 4.83e-01 95.8% 84.4%
3rkvA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.71 40.0 3.72e-01 97.5% 44.9%
1nafA02 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 44.0 5.18e-01 98.3% 89.4%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 40.0 5.13e-01 86.6% 98.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 47.0 5.36e-01 96.6% 92.4%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 40.0 3.43e-01 99.2% 37.1%
3rc3A05 1.20.58.1080 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 38.0 3.97e-01 100.0% 58.4%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.66 46.0 5.25e-01 90.8% 94.4%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.65 47.0 3.18e-01 95.8% 22.0%
1rq0A01 6.10.140.160 Special › Helix non-globular › Helix Hairpins › 0.62 38.0 4.62e-01 70.6% 89.2%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.62 40.0 4.69e-01 98.3% 90.8%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 45.0 4.91e-01 99.2% 90.1%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 44.0 4.71e-01 100.0% 87.1%
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 0.61 42.0 4.38e-01 98.3% 77.1%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.60 36.0 4.13e-01 99.2% 82.4%
1uurA01 1.20.58.240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › STAT; domain 1 0.60 47.0 4.90e-01 98.3% 89.1%
1k90B03 1.20.140.60 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.60 43.0 4.37e-01 90.8% 76.5%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.58 43.0 4.05e-01 77.3% 65.5%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 45.0 4.50e-01 98.3% 78.7%
4gyvE00 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.57 47.0 3.83e-01 99.2% 48.4%
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.55 45.0 4.29e-01 86.6% 81.3%
1txdA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.55 48.0 3.83e-01 100.0% 48.5%
1aluA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 45.0 4.08e-01 86.6% 66.9%
3d85C00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 41.0 3.99e-01 82.4% 70.7%
4dkcB00 1.20.1250.80 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-34 0.54 43.0 3.88e-01 97.5% 61.9%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 49.0 4.06e-01 100.0% 94.3%
1yo7A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 44.0 4.40e-01 86.6% 92.5%
5nohA00 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.54 33.0 3.47e-01 95.0% 68.0%
2oerA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 39.0 3.44e-01 95.0% 50.3%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 40.0 3.98e-01 100.0% 76.9%
3g7rA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 36.0 3.10e-01 99.2% 43.9%
4gouA03 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.52 47.0 3.93e-01 98.3% 58.4%
4iu9B01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.52 37.0 3.06e-01 100.0% 39.3%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 47.0 4.44e-01 98.3% 92.4%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.52 41.0 4.30e-01 99.2% 90.0%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.52 47.0 3.89e-01 100.0% 75.7%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.52 42.0 4.33e-01 100.0% 89.7%
2fzfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 46.0 4.24e-01 96.6% 86.0%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 46.0 4.18e-01 95.8% 81.6%
4qgpB00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.51 35.0 3.66e-01 85.7% 79.4%
3fseB02 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.50 46.0 4.34e-01 98.3% 88.9%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2464385 192.27.1.0 ↗ alpha bundles › Long alpha-hairpin › Helical hairpin in putative tRNA methyltransferase › Helical hairpin in putative tRNA methyltransferase 0.81 42.0 5.75e-01 95.0% 96.8%
3795985 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.79 47.0 5.55e-01 99.2% 83.5%
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 0.76 62.0 4.69e-01 84.9% 60.0%
3895663 109.4.1.95 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2 0.74 42.0 3.65e-01 95.8% 38.8%
3243299 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.73 41.0 5.28e-01 97.5% 95.7%
3796589 604.12.1.1 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT 0.73 41.0 4.50e-01 98.3% 67.0%
3931593 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.71 41.0 4.89e-01 98.3% 83.7%
3622515 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.70 40.0 4.69e-01 95.0% 78.8%
3742811 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.70 47.0 4.80e-01 99.2% 70.4%
4958743 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 47.0 4.82e-01 95.8% 75.7%
4958744 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 46.0 4.82e-01 95.8% 78.2%
5050371 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 46.0 4.91e-01 95.8% 84.8%
4959990 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.64 47.0 4.58e-01 97.5% 69.2%
3924651 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 44.0 4.79e-01 98.3% 88.4%
3458224 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 41.0 4.32e-01 99.2% 71.8%
3231982 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.63 43.0 3.86e-01 100.0% 50.0%
5067572 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.62 45.0 4.75e-01 99.2% 83.8%
4983442 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.62 42.0 4.69e-01 99.2% 88.4%
4935676 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.62 42.0 4.42e-01 99.2% 76.4%
4944708 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.61 42.0 4.70e-01 98.3% 93.3%
4983440 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.61 40.0 4.55e-01 96.6% 90.0%
3280999 101.1.2.135 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.60 45.0 4.08e-01 77.3% 83.9%
3291034 3271.1.1.1 ↗ alpha arrays › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › Ntox28 0.59 44.0 4.91e-01 98.3% 96.8%
3245526 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 44.0 4.66e-01 99.2% 88.6%
3516367 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.57 47.0 4.55e-01 86.6% 88.9%
3941051 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.57 46.0 4.06e-01 97.5% 59.4%
3359095 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.56 34.0 4.07e-01 99.2% 94.7%
3886417 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.56 47.0 3.95e-01 100.0% 53.5%
4288811 109.4.1.2255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30195, PF30196 0.56 52.0 3.16e-01 99.2% 20.6%
3593736 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.56 40.0 4.43e-01 74.8% 97.0%
4674738 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.56 51.0 4.10e-01 100.0% 53.2%
3510145 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.55 48.0 4.15e-01 99.2% 61.1%
4013672 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.55 38.0 4.18e-01 71.4% 90.0%
3177931 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.55 49.0 3.90e-01 100.0% 49.6%
3567477 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.55 47.0 3.83e-01 100.0% 50.0%
3874130 133.1.1.5 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › DH_Alsin 0.55 50.0 4.10e-01 100.0% 55.7%
3800960 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.54 49.0 3.85e-01 100.0% 48.9%
3617707 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.54 48.0 3.94e-01 100.0% 55.1%
3250955 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.54 39.0 2.88e-01 73.9% 33.0%
3298761 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.53 49.0 3.87e-01 100.0% 87.1%
4093008 192.29.1.157 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › MG280 0.52 41.0 3.38e-01 84.0% 57.3%
222003 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.52 48.0 4.04e-01 100.0% 61.3%
3515526 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.52 45.0 4.36e-01 100.0% 81.5%
3276862 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.52 49.0 3.94e-01 100.0% 61.9%
3527488 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.52 46.0 3.99e-01 99.2% 84.2%
3242228 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.52 45.0 4.57e-01 100.0% 95.8%
3588519 101.1.2.49 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.51 47.0 4.13e-01 96.6% 83.0%
3940046 4156.1.1.0 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.51 45.0 3.62e-01 98.3% 85.5%
3795777 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.50 44.0 4.42e-01 100.0% 92.0%
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 0.50 44.0 4.60e-01 100.0% 100.0%
D4 medium residues 498-540_562-593
PDB
Domain cluster: rep: DNA_polymerase__YP_009316112__Anticarsia_gemmatalis_multiple_nucleopolyhedrovirus__268591__D473-499_523-556
D5 medium residues 541-561_648-777
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 53.9 1.90e-14 89.4% 27.8%
D6 medium residues 778-836_857-966_1003-1035
PDB
Domain cluster: rep: hypothetical_protein_MIV120R__YP_654692__Invertebrate_iridescent_virus_3__345201__D821-880_935-1042