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DNA_polymerase

Euk-Vir

Diatraea_saccharalis_granulovirus

DNA_polymerase__YP_009182295__Diatraea_saccharalis_granulovirus__1675862

Identity

Accession:
YP_009182295 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

85.2 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Betabaculovirus› Diatraea_saccharalis_granulovirus

TaxID: 1675862

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 176-415
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 32.0 1.40e-07 90.0% 65.6%
PF03104.26 DNA_pol_B_exo1 90.9 1.20e-25 72.5% 72.3%
D2 medium residues 1-175
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D3 medium residues 418-475_477-636
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 61.3 1.10e-16 81.2% 31.8%
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.76 23.0 4.58e-01 88.1% 100.0%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 21.0 3.72e-01 90.4% 76.7%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 30.0 4.63e-01 95.0% 92.4%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 25.0 4.43e-01 85.8% 100.0%
2p4vA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.64 24.0 3.86e-01 81.7% 92.1%
2x1lA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.63 28.0 3.18e-01 98.2% 51.7%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.58 28.0 3.41e-01 95.4% 67.6%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.57 27.0 3.59e-01 95.0% 83.8%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.55 30.0 3.70e-01 95.9% 82.7%
4p9tA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 30.0 3.95e-01 96.8% 98.3%
2a2cA03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.53 31.0 3.79e-01 91.7% 89.1%
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 0.52 20.0 2.81e-01 73.9% 69.9%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 23.0 2.88e-01 95.9% 66.0%
4dkcB00 1.20.1250.80 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-34 0.51 25.0 2.98e-01 97.2% 65.6%
3purA03 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 22.0 2.93e-01 96.3% 73.6%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4597007 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.92 19.0 5.27e-01 89.0% 100.0%
4565383 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.90 21.0 5.28e-01 91.3% 100.0%
4544002 192.6.1.1 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATP-synt_DE 0.90 21.0 5.22e-01 91.7% 100.0%
3795985 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.82 25.0 4.25e-01 95.0% 74.1%
4932480 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 0.82 48.0 4.79e-01 72.0% 58.2%
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 0.81 26.0 5.01e-01 82.6% 100.0%
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 0.81 63.0 4.65e-01 100.0% 35.5%
None — 0.79 62.0 4.28e-01 100.0% 27.3%
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 0.79 61.0 5.49e-01 100.0% 60.7%
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 0.79 54.0 5.32e-01 93.6% 65.1%
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 0.78 48.0 4.85e-01 94.0% 61.9%
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 0.77 58.0 5.47e-01 99.1% 66.4%
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 0.77 57.0 5.44e-01 99.1% 66.4%
3742811 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.76 28.0 3.87e-01 93.6% 64.3%
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 0.76 58.0 5.09e-01 98.2% 55.7%
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 0.76 53.0 5.04e-01 85.8% 62.4%
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 0.76 47.0 4.63e-01 85.3% 58.3%
3801150 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 0.75 51.0 4.55e-01 83.9% 51.2%
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 0.74 61.0 5.32e-01 100.0% 59.4%
4958744 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.73 31.0 4.35e-01 93.6% 79.1%
4958743 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.72 31.0 4.26e-01 93.6% 76.5%
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 0.72 49.0 4.72e-01 85.8% 61.2%
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 0.72 63.0 4.28e-01 100.0% 29.5%
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 0.71 50.0 4.57e-01 72.0% 60.4%
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 0.70 50.0 4.64e-01 82.6% 59.6%
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 0.70 45.0 4.45e-01 85.3% 61.8%
3253283 192.5.1.14 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.69 30.0 4.50e-01 96.3% 92.6%
3924651 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.69 28.0 4.14e-01 96.3% 84.2%
4000281 192.20.1.0 ↗ alpha bundles › Long alpha-hairpin › helical hairpin domain in transcriptional anti-activator ExsD › helical hairpin domain in transcriptional anti-activator ExsD 0.68 29.0 4.25e-01 98.6% 86.0%
4958742 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 29.0 3.84e-01 95.0% 69.6%
4976290 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.66 26.0 4.22e-01 95.0% 97.5%
3876247 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 30.0 3.96e-01 95.9% 82.5%
5056427 3843.1.1.38 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › T4SS_pilin 0.61 28.0 3.96e-01 91.7% 86.4%
5032045 4163.1.1.0 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.61 27.0 3.99e-01 97.7% 92.0%
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 32.0 3.96e-01 94.5% 85.0%
4108773 142.1.1.1 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r1_2,Sigma70_r2 0.54 32.0 2.77e-01 73.9% 38.5%
4998819 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.52 29.0 3.70e-01 71.6% 90.8%
3601853 604.7.1.0 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.52 31.0 3.68e-01 96.3% 86.2%
3565062 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.51 29.0 3.57e-01 95.4% 86.4%
D4 medium residues 637-727
PDB
Domain cluster: rep: DNA_polymerase__YP_003422477__Pseudalatia_unipuncta_granulovirus__36355__D676-752
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 26.2 4.90e-06 97.8% 11.5%
D5 medium residues 890-932_971-1025
PDB
Domain cluster: rep: polymerase__YP_002854676__Euproctis_pseudoconspersa_nucleopolyhedrovirus__307467__D973-1018_1035-1067
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4942434 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.54 37.0 3.80e-01 79.6% 73.7%
4991403 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.52 38.0 2.60e-01 76.5% 36.7%
5054303 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.51 33.0 3.60e-01 80.6% 80.0%