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DNA_polymerase

Euk-Vir

Flamingopox_virus_FGPVKD09

DNA_polymerase__YP_009448013__Flamingopox_virus_FGPVKD09__2059380

Identity

Accession:: YP_009448013 ↗
Protein ID:: DNA_polymerase
Kingdom:: euk

Quality

80.0 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Avipoxvirus› Flamingopox_virus_FGPVKD09

TaxID: 2059380

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 159-324_434-461

PDB

Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_401712__Human_gammaherpesvirus_4__10376__D288-457

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03104.26 best	DNA_pol_B_exo1	117.3	1.00e-33	90.2%	69.4%
PF08408.17	DNA_pol_B_3	48.3	1.60e-12	41.2%	42.2%

D2 high residues 330-419

PDB

Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_009162448__Salmon_gill_poxvirus__1680908__D388-474

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF08408.17 best	DNA_pol_B_3	79.6	3.50e-22	95.6%	65.6%

D3 high residues 825-980

PDB

Domain cluster: rep: IMGVR_UViG_3300021255_003095-3300021255-Ga0223825_1010595139__D209-342

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	89.7	2.70e-25	93.0%	30.7%

D4 medium residues 1-43_113-153

PDB

D5 medium residues 44-65_82-112

PDB

Domain cluster: representative

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1vc9A01	3.90.79.10	Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase	0.57	45.0	3.70e-01	100.0%	96.7%
3nlcA01	3.30.70.2700	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.54	44.0	3.99e-01	96.2%	78.9%
3tupA02	3.30.70.380	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain	0.53	38.0	3.28e-01	79.2%	77.1%
1pu1A00	3.30.300.100	Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like	0.51	37.0	3.17e-01	79.2%	56.0%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
None	—		0.52	43.0	2.46e-01	100.0%	8.5%
3313182	327.11.1.0 ↗	a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II)	0.51	35.0	3.36e-01	77.4%	81.4%

D6 medium residues 66-81_462-513_557-665

PDB

Domain cluster: rep: IMGVR_UViG_3300048031_000811-3300048031-Ga0494182_008429_2395_4416__D190-244_288-384

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	84.6	9.00e-24	62.2%	17.4%

CATH (16)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4iloA00	1.10.287.1490	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.72	29.0	2.63e-01	91.5%	29.2%
4q20A01	1.10.287.130	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain	0.71	30.0	4.49e-01	92.7%	87.8%
1fpoC02	1.20.1280.20	Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain	0.69	34.0	4.80e-01	87.6%	94.5%
4fvmA04	6.10.10.100	Special › Helix non-globular › Helicase, Ruva Protein; domain 3 ›	0.69	21.0	3.71e-01	90.4%	95.7%
4wzxA01	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.69	28.0	4.25e-01	84.2%	89.3%
1rv2D04	1.10.287.690	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain	0.68	28.0	4.39e-01	98.3%	97.1%
4fxdA04	3.90.1600.10	Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain	0.67	51.0	5.46e-01	91.0%	90.2%
3u3iA02	1.20.58.1110	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.65	34.0	4.22e-01	87.6%	80.6%
2ic6A00	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.64	26.0	3.90e-01	97.2%	88.7%
6z01B03	1.10.132.10	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 ›	0.63	31.0	3.35e-01	80.2%	53.9%
1z0pA00	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.62	26.0	3.89e-01	91.0%	93.2%
2k3iA01	3.30.70.860	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.58	20.0	2.73e-01	91.0%	56.5%
1s35A01	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.55	30.0	3.95e-01	86.4%	95.0%
1fpqA02	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.54	22.0	2.56e-01	84.2%	46.5%
1ydxA02	1.10.287.1120	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein	0.52	26.0	3.58e-01	90.4%	94.4%
4etrB00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.50	31.0	3.73e-01	84.7%	89.3%

ECOD (26)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3605750	2484.1.1.34 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1	0.74	66.0	4.07e-01	92.7%	72.9%
None	—		0.74	65.0	4.12e-01	92.7%	77.4%
5073085	3755.3.1.0 ↗	alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin	0.72	30.0	3.18e-01	93.8%	43.9%
5011084	604.3.1.0 ↗	alpha bundles › Spectrin repeat-like › BAG domain › BAG domain	0.72	32.0	4.80e-01	86.4%	95.0%
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	0.71	40.0	3.94e-01	90.4%	50.5%
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	0.69	61.0	4.28e-01	91.0%	37.9%
None	—		0.69	66.0	4.33e-01	100.0%	71.2%
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	0.69	52.0	4.17e-01	76.8%	52.5%
None	—		0.68	65.0	4.27e-01	100.0%	73.1%
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	0.67	64.0	4.17e-01	100.0%	69.3%
5081021	5067.1.1.0 ↗	alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain	0.66	40.0	4.37e-01	90.4%	71.7%
4972474	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.66	63.0	4.11e-01	100.0%	71.4%
3684015	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.66	32.0	4.20e-01	97.2%	82.0%
3949475	5067.1.1.0 ↗	alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain	0.65	37.0	3.52e-01	90.4%	46.2%
5019480	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	0.65	62.0	3.97e-01	100.0%	69.9%
4992256	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.64	32.0	4.26e-01	84.7%	85.9%
3629711	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.62	34.0	4.13e-01	84.2%	79.2%
3903860	150.1.1.0 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin	0.60	36.0	3.94e-01	85.3%	71.0%
3626133	601.1.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin	0.60	30.0	3.51e-01	85.3%	65.6%
3346653	604.6.1.1 ↗	alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT	0.60	30.0	3.83e-01	87.0%	81.0%
3740645	604.6.1.1 ↗	alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT	0.60	30.0	4.11e-01	87.0%	94.4%
5046003	4070.1.1.0 ↗	alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like	0.57	40.0	3.97e-01	91.0%	66.8%
3652633	3930.1.1.0 ↗	alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase	0.54	34.0	3.98e-01	91.0%	86.2%
5011658	4070.1.1.0 ↗	alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like	0.53	39.0	3.84e-01	91.0%	69.6%
3549089	109.4.1.1363 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT, HEAT_EZ, TPR_IMB1	0.52	33.0	2.97e-01	96.6%	45.8%
3484828	150.1.1.0 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin	0.52	34.0	3.64e-01	87.6%	75.5%

D7 medium residues 532-556_666-824

PDB

Domain cluster: rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	142.7	2.20e-41	87.5%	30.7%
PF00136.27	DNA_pol_B	28.2	1.20e-06	14.7%	5.5%