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DNA_polymerase

Euk-Vir

Micromonas_pusilla_virus_12T

DNA_polymerase__YP_007676285__Micromonas_pusilla_virus_12T__755272

Identity

Accession:
YP_007676285 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

84.8 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Prasinovirus› Micromonas_pusilla_virus_12T

TaxID: 755272

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 3-178
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D2 high residues 188-418
PDB
Domain cluster: rep: B-family_DNA_polymerase__YP_009507574__Heterosigma_akashiwo_virus_01__97195__D190-438
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 106.0 3.10e-30 78.8% 73.1%
D3 high residues 748-883
PDB
Domain cluster: rep: hypothetical_protein_MIV120R__YP_654692__Invertebrate_iridescent_virus_3__345201__D821-880_935-1042
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 74.4 1.10e-20 86.0% 23.4%
D4 high residues 900-941
PDB
D5 medium residues 419-488_532-602
PDB
Domain cluster: rep: IMGVR_UViG_3300048031_000811-3300048031-Ga0494182_008429_2395_4416__D190-244_288-384
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 50.7 1.90e-13 53.9% 15.9%
PF00136.27 DNA_pol_B 24.1 2.10e-05 40.4% 11.9%
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.79 30.0 4.50e-01 73.8% 78.5%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 33.0 5.16e-01 88.7% 96.7%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.72 38.0 4.93e-01 96.5% 88.0%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.72 65.0 6.32e-01 99.3% 87.6%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.71 38.0 4.75e-01 95.0% 85.1%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 35.0 4.68e-01 92.2% 89.3%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.66 35.0 4.04e-01 84.4% 69.9%
2i0mA01 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 0.62 41.0 4.64e-01 97.2% 87.7%
1sumB02 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 0.62 42.0 4.56e-01 100.0% 81.4%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.62 39.0 4.63e-01 99.3% 96.7%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.61 35.0 4.42e-01 97.9% 98.7%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 38.0 4.50e-01 95.0% 92.6%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.60 35.0 3.31e-01 89.4% 46.0%
1ugoA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.60 40.0 4.77e-01 98.6% 97.0%
1w0bA01 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.60 37.0 4.36e-01 99.3% 93.5%
4nwpD00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.60 37.0 3.66e-01 98.6% 57.7%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 30.0 3.95e-01 76.6% 94.4%
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.58 40.0 4.29e-01 96.5% 81.5%
4qndA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.57 34.0 3.90e-01 97.2% 81.4%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.57 42.0 4.63e-01 97.9% 95.5%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.57 37.0 4.22e-01 95.0% 89.2%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.57 40.0 4.48e-01 95.7% 91.1%
1lqsL01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 34.0 3.96e-01 96.5% 85.0%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.54 29.0 3.61e-01 89.4% 82.4%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 40.0 4.32e-01 99.3% 94.9%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.51 33.0 3.86e-01 84.4% 91.3%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None — 0.92 89.0 5.52e-01 100.0% 28.9%
3628202 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 0.91 88.0 5.43e-01 100.0% 27.5%
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 0.91 87.0 5.40e-01 100.0% 31.1%
None — 0.90 87.0 5.41e-01 100.0% 29.1%
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 0.90 86.0 5.35e-01 100.0% 33.3%
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 0.87 83.0 5.51e-01 100.0% 46.4%
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 0.84 66.0 5.35e-01 82.3% 61.2%
3466667 2484.1.1.161 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.82 79.0 4.92e-01 100.0% 25.7%
4438700 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.75 43.0 5.43e-01 98.6% 94.1%
55142 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.73 38.0 4.90e-01 94.3% 84.9%
3934523 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.66 39.0 4.68e-01 93.6% 87.4%
3183050 5067.1.1.5 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Sterol-sensing 0.65 46.0 3.73e-01 100.0% 40.0%
3601007 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.65 36.0 2.48e-01 95.0% 16.1%
3657213 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 0.65 28.0 4.45e-01 86.5% 100.0%
4967525 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.62 35.0 2.73e-01 98.6% 25.3%
3469551 3978.1.1.0 ↗ alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase 0.60 47.0 4.14e-01 100.0% 58.0%
4051050 3978.1.1.0 ↗ alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase 0.59 47.0 4.13e-01 100.0% 58.0%
3466019 3978.1.1.2 ↗ alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › FA_hydroxylase 0.59 46.0 3.89e-01 100.0% 49.4%
3755802 604.12.1.98 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › NKAIN 0.58 39.0 4.50e-01 97.2% 91.4%
2625677 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.57 42.0 4.63e-01 97.9% 95.5%
3484908 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 38.0 4.41e-01 95.0% 92.4%
3707921 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.56 39.0 4.37e-01 97.2% 90.0%
3576275 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.55 39.0 4.08e-01 96.5% 79.2%
4002586 622.4.1.31 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › TPR_SYVN1_N 0.54 41.0 3.69e-01 98.6% 56.9%
3615244 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 37.0 3.54e-01 95.7% 60.6%
3991109 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.54 42.0 4.25e-01 97.9% 81.4%
3493397 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.52 41.0 3.66e-01 96.5% 60.0%
3684239 4967.1.1.0 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.52 31.0 2.89e-01 100.0% 42.6%
4013285 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.52 40.0 3.35e-01 98.6% 47.9%
3621305 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.51 40.0 3.96e-01 97.9% 76.7%
3310955 630.1.1.1 ↗ a+b complex topology › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › Rubis-subs-bind 0.51 43.0 4.45e-01 93.6% 95.4%
D6 medium residues 489-531_603-747
PDB
Domain cluster: rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 125.9 2.80e-36 83.0% 34.4%
PF00136.27 DNA_pol_B 39.9 3.40e-10 20.7% 7.5%