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DNA_polymerase

Euk-Vir

Operophtera_brumata_nucleopolyhedrovirus

DNA_polymerase__YP_009552625__Operophtera_brumata_nucleopolyhedrovirus__1046267

Identity

Accession:: YP_009552625 ↗
Protein ID:: DNA_polymerase
Kingdom:: euk

Quality

84.6 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Operophtera_brumata_nucleopolyhedrovirus

TaxID: 1046267

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 748-807_819-912

PDB

Domain cluster: rep: hypothetical_protein_MIV120R__YP_654692__Invertebrate_iridescent_virus_3__345201__D821-880_935-1042

D2 medium residues 1-183

PDB

Domain cluster: rep: DNA_polymerase__YP_009666761__Mythimna_unipuncta_nucleopolyhedrovirus__447897__D1-67_114-188

D3 medium residues 184-273

PDB

Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_010088005__Lymphocystis_disease_virus_4__2704413__D159-241

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03104.26 best	DNA_pol_B_exo1	37.1	3.40e-09	100.0%	38.4%

D4 medium residues 274-342

PDB

Domain cluster: rep: DNA_polymerase__YP_008378438__Choristoneura_rosaceana_nucleopolyhedrovirus__58094__D271-327

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03104.26 best	DNA_pol_B_exo1	28.3	1.60e-06	100.0%	28.5%

D5 medium residues 343-406

PDB

Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009342373__Spheniscid_alphaherpesvirus_1__2560777__D504-588

D6 medium residues 407-471

PDB

Domain cluster: representative

CATH (8)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4fvmA04	6.10.10.100	Special › Helix non-globular › Helicase, Ruva Protein; domain 3 ›	0.83	57.0	6.54e-01	87.7%	100.0%
3gpvA00	1.10.1660.10	Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 ›	0.58	40.0	3.43e-01	73.8%	73.5%
1t3aA00	3.90.1240.10	Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like"	0.57	40.0	2.52e-01	76.9%	50.7%
3rk6A00	1.25.40.180	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.55	44.0	3.16e-01	92.3%	65.9%
8be0A01	3.40.91.90	Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	0.54	41.0	3.10e-01	87.7%	91.1%
2fd5A02	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.52	41.0	3.33e-01	87.7%	87.1%
2vx7A00	3.20.20.80	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases	0.51	40.0	2.52e-01	86.2%	40.9%
6k9pB02	1.20.1300.20	Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Peptidase C65 Otubain, subdomain 2	0.50	41.0	3.27e-01	96.9%	75.0%

ECOD (25)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3368695	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.86	56.0	3.38e-01	84.6%	11.3%
3710418	2484.1.1.34 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1	0.84	55.0	3.35e-01	84.6%	11.7%
5025208	2484.1.1.34 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1	0.81	54.0	3.61e-01	87.7%	19.6%
4888481	2484.1.1.34 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1	0.80	60.0	3.91e-01	100.0%	19.5%
3496492	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.73	57.0	3.66e-01	98.5%	18.6%
3206356	304.114.1.0 ↗	a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain	0.72	56.0	3.41e-01	98.5%	13.5%
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	0.64	58.0	3.29e-01	100.0%	30.6%
3938116	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.59	45.0	3.11e-01	86.2%	50.2%
3490651	141.1.1.0 ↗	alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases	0.59	48.0	2.96e-01	92.3%	52.6%
3590899	2007.1.2.11 ↗	a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_4	0.58	39.0	2.91e-01	70.8%	80.9%
3887540	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.57	44.0	2.60e-01	86.2%	27.4%
4043003	601.7.1.6 ↗	alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase	0.56	41.0	3.06e-01	80.0%	31.8%
4033688	101.1.2.92 ↗	alpha arrays › HTH › HTH › winged helix domain › HTH_11	0.54	30.0	3.00e-01	83.1%	50.0%
3871096	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.54	40.0	2.62e-01	81.5%	29.7%
3530542	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.54	39.0	2.63e-01	81.5%	37.6%
5069346	219.1.1.13 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core	0.54	43.0	3.07e-01	87.7%	68.8%
3560659	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.54	40.0	2.61e-01	81.5%	31.5%
3474413	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.53	39.0	2.52e-01	83.1%	28.6%
3940179	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.52	35.0	2.62e-01	70.8%	49.5%
3687833	5073.1.1.18 ↗	alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain M › Hydrolase	0.52	43.0	2.58e-01	100.0%	63.8%
3532358	206.1.1.1 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase	0.51	42.0	2.72e-01	95.4%	92.0%
3395806	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.51	39.0	2.60e-01	86.2%	55.1%
3251651	2003.1.2.18 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain	0.50	41.0	2.50e-01	100.0%	67.3%
3922833	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.50	40.0	2.80e-01	100.0%	55.6%
3612163	4177.1.1.0 ↗	alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like	0.50	38.0	2.73e-01	87.7%	60.0%

D7 medium residues 472-637

PDB

Domain cluster: rep: DNA_polymerase__YP_010086932__Cryptophlebia_peltastica_nucleopolyhedrovirus__2304025__D494-537_560-649

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	58.6	7.20e-16	95.2%	33.8%

D8 medium residues 638-737

PDB

Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009552191__Malacosoma_neustria_nucleopolyhedrovirus__38012__D557-567_668-765

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	35.2	8.70e-09	100.0%	17.9%