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DNA_polymerase

Euk-Vir

Bohle_iridovirus

DNA_polymerase__YP_009506722__Bohle_iridovirus__100220

Identity

Accession:
YP_009506722 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

80.9 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Iridoviridae› Ranavirus› Bohle_iridovirus

TaxID: 100220

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 high residues 2-162_419-431
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D2 high residues 519-584
PDB
Domain cluster: rep: DNA_polymerase__YP_006347653__European_catfish_virus__84739__D519-584
D3 medium residues 164-251
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_010088005__Lymphocystis_disease_virus_4__2704413__D159-241
D4 medium residues 389-418_602-663
PDB
Domain cluster: rep: DNA_polymerase__YP_008052566__Phaeocystis_globosa_virus__251749__D724-746_869-928
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 67.5 1.40e-18 91.3% 14.1%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.89 83.0 6.86e-01 100.0% 90.2%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.73 49.0 5.31e-01 88.0% 81.8%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.73 55.0 5.75e-01 88.0% 86.7%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.71 48.0 5.31e-01 81.5% 85.3%
4xriA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.71 56.0 3.18e-01 89.1% 8.8%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.71 57.0 5.95e-01 92.4% 92.9%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 53.0 4.46e-01 81.5% 86.6%
1txdA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.67 57.0 4.19e-01 91.3% 51.1%
4akgA04 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.67 58.0 4.78e-01 97.8% 54.5%
3vkgB03 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.67 60.0 4.98e-01 97.8% 59.6%
3fseB02 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.66 55.0 4.60e-01 85.9% 87.5%
5ux1D00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.66 53.0 4.08e-01 85.9% 67.0%
2fzfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.65 55.0 4.58e-01 88.0% 86.7%
2hroA02 1.10.274.10 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › PtsI, HPr-binding domain 0.65 50.0 4.47e-01 92.4% 58.6%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.65 51.0 5.20e-01 89.1% 82.6%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.65 56.0 5.63e-01 92.4% 95.6%
3nvoB02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.64 55.0 5.07e-01 92.4% 87.1%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.63 54.0 4.58e-01 91.3% 93.1%
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.62 52.0 4.46e-01 88.0% 76.3%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.61 54.0 4.27e-01 93.5% 93.6%
3zciA00 1.20.58.1660 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 55.0 4.30e-01 98.9% 100.0%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 51.0 4.89e-01 93.5% 83.3%
1zymA02 1.10.274.10 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › PtsI, HPr-binding domain 0.61 48.0 4.31e-01 93.5% 61.9%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.60 49.0 4.74e-01 88.0% 84.3%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.60 50.0 4.42e-01 88.0% 79.2%
1nzeA00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.60 46.0 4.32e-01 89.1% 67.0%
4qndA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.58 46.0 4.55e-01 98.9% 82.5%
3gi7A00 1.20.1270.180 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.57 43.0 4.18e-01 79.3% 77.7%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.57 47.0 3.99e-01 89.1% 55.6%
7vwtA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 49.0 3.43e-01 97.8% 81.9%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.56 47.0 4.69e-01 92.4% 93.8%
1vdyA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 46.0 4.02e-01 90.2% 78.6%
6ldkA01 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.55 47.0 3.84e-01 95.7% 68.6%
2zopA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.54 45.0 4.21e-01 90.2% 100.0%
3f4mA00 1.20.1440.160 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like 0.53 43.0 3.64e-01 88.0% 81.8%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.99 96.0 5.53e-01 100.0% 28.0%
None — 0.98 95.0 5.49e-01 100.0% 29.4%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.97 94.0 5.39e-01 100.0% 27.4%
3605750 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.90 85.0 4.75e-01 100.0% 39.2%
4022366 2484.1.1.161 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 77.0 4.54e-01 100.0% 29.8%
4954644 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.80 57.0 5.16e-01 73.9% 100.0%
3959202 1152.1.1.2 ↗ a+b three layers › a+b domain in conserved hypothetical protein Rv3899c › a+b domain in conserved hypothetical protein Rv3899c › a+b domain in conserved hypothetical protein Rv3899c › PF27215 0.76 59.0 4.39e-01 81.5% 84.5%
3717958 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.76 57.0 3.34e-01 78.3% 28.6%
4054419 604.12.1.78 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › FUSC 0.74 61.0 4.94e-01 87.0% 89.7%
5011084 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.74 56.0 6.00e-01 85.9% 91.3%
4026036 109.4.1.574 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NOC3p 0.72 55.0 4.11e-01 87.0% 34.0%
3934154 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.70 52.0 5.46e-01 82.6% 84.7%
4801290 601.1.2.4 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_R4 0.69 50.0 4.30e-01 76.1% 91.7%
4941690 5067.1.1.2 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › SecD_SecF 0.68 63.0 4.87e-01 100.0% 51.5%
5067364 5067.1.1.2 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › SecD_SecF 0.68 63.0 4.76e-01 100.0% 47.3%
5034897 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.68 57.0 4.32e-01 90.2% 73.5%
3641813 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.68 55.0 5.49e-01 85.9% 84.2%
5053883 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.67 54.0 4.31e-01 89.1% 44.6%
3944793 601.19.1.41 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › YicC-like_C 0.66 50.0 4.15e-01 79.3% 84.5%
4009669 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.66 50.0 3.90e-01 79.3% 49.2%
4927596 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.66 55.0 4.82e-01 88.0% 66.2%
3901272 174.1.1.87 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tmp39 0.66 56.0 3.77e-01 91.3% 93.6%
3658685 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.66 53.0 4.94e-01 87.0% 90.4%
3740645 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.65 53.0 5.38e-01 85.9% 90.0%
3621305 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.65 54.0 4.56e-01 89.1% 78.0%
3528863 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.65 53.0 4.94e-01 88.0% 73.9%
3409326 3930.1.1.6 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › Dicer_PBD 0.64 53.0 4.55e-01 85.9% 90.4%
3690615 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.64 52.0 4.63e-01 95.7% 62.3%
3267005 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.63 52.0 5.01e-01 93.5% 77.1%
55069 603.1.1.1 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin 0.63 51.0 4.87e-01 88.0% 87.2%
4654652 633.21.1.23 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CD20 0.63 52.0 4.49e-01 88.0% 80.0%
3688139 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.63 47.0 4.33e-01 89.1% 60.0%
2774879 4244.1.1.2 ↗ a/b three-layered sandwiches › EreA/ChaN-like › EreA/ChaN-like › EreA/ChaN-like › Erythro_esteras 0.63 54.0 3.59e-01 97.8% 63.5%
3586824 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.62 50.0 3.21e-01 85.9% 28.1%
4012037 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.62 53.0 4.14e-01 89.1% 60.0%
3516004 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.62 51.0 3.48e-01 87.0% 34.4%
3289734 109.4.1.637 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF2339 0.62 49.0 3.39e-01 88.0% 25.2%
3622896 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.62 56.0 4.84e-01 97.8% 86.4%
3256951 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.62 48.0 4.49e-01 100.0% 67.8%
3933812 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.61 48.0 3.62e-01 82.6% 67.9%
5039404 604.2.1.0 ↗ alpha bundles › Spectrin repeat-like › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 0.61 42.0 4.56e-01 81.5% 88.0%
3172226 603.1.1.17 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › SNARE 0.61 55.0 3.98e-01 100.0% 67.2%
3549954 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.60 51.0 3.45e-01 89.1% 34.3%
3233878 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.60 50.0 4.44e-01 88.0% 84.8%
3785237 601.1.3.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › A middle domain of Talin 1 › GCIP_N 0.60 53.0 4.05e-01 94.6% 52.8%
3576407 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.59 48.0 4.48e-01 89.1% 92.2%
5051058 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.58 53.0 4.07e-01 98.9% 71.0%
4141957 140.1.1.4 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › tRNA-synt_1e,DALR_2 0.58 48.0 3.86e-01 92.4% 47.4%
5046163 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.56 48.0 4.28e-01 95.7% 85.2%
4111534 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.54 46.0 3.30e-01 100.0% 58.1%
3970258 5069.1.1.5 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cyt_bd_oxida_II 0.54 48.0 4.02e-01 95.7% 80.7%
D5 medium residues 460-512_664-787
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D490-509_716-834
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 69.5 3.50e-19 70.6% 29.6%
PF00136.27 DNA_pol_B 44.2 1.70e-11 31.6% 9.0%
D6 medium residues 827-922
PDB
Domain cluster: rep: archaeal_DNA_polymerase_I__YP_009021128__Anopheles_minimus_iridovirus__1465751__D870-955