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DNA_polymerase_catalytic_subunit

Euk-Vir

Testudinid_alphaherpesvirus_3

DNA_polymerase_catalytic_subunit__YP_009176907__Testudinid_alphaherpesvirus_3__2560801

Identity

Accession:: YP_009176907 ↗
Protein ID:: DNA_polymerase_catalytic_subunit
Kingdom:: euk

Quality

81.9 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Scutavirus› Testudinid_alphaherpesvirus_3

TaxID: 2560801

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 306-528

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
PF10108.16 best	DNA_pol_B_exo2	26.5	7.00e-06	87.0%	64.6%
PF03104.26	DNA_pol_B_exo1	169.1	1.60e-49	77.6%	74.8%

D2 high residues 875-951_994-1002_1036-1108

PDB

Domain cluster: rep: DNA_polymerase_catalytic_subunit__NP_073324__Meleagrid_alphaherpesvirus_1__37108__D926-999_1042-1063_1105-1149

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	24.7	1.30e-05	52.2%	13.7%

CATH (16)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2gv9B06	1.10.132.60	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain	0.90	75.0	6.82e-01	86.2%	99.5%
4fxdA06	1.10.132.60	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain	0.70	58.0	5.83e-01	85.5%	99.4%
3iayA07	1.10.132.60	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain	0.66	54.0	5.60e-01	86.2%	99.3%
1tgoA05	1.10.132.60	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain	0.63	54.0	5.29e-01	88.1%	92.8%
1dk8A02	1.10.167.10	Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2	0.60	26.0	3.39e-01	81.1%	71.8%
2xseA00	1.20.120.1440	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain	0.59	44.0	4.48e-01	86.8%	78.6%
4ikhA02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.56	33.0	3.67e-01	83.6%	72.4%
3ubkB02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.56	31.0	3.39e-01	81.8%	65.6%
5cwhA01	1.25.10.10	Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant	0.54	29.0	2.99e-01	83.0%	50.0%
4xaxB02	1.20.58.1290	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain	0.53	33.0	4.08e-01	84.9%	100.0%
2oduA02	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.52	31.0	3.58e-01	78.6%	83.8%
3zsuA00	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	0.52	29.0	3.26e-01	73.6%	69.5%
2gfhA02	1.20.120.710	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain	0.52	26.0	3.22e-01	73.6%	80.2%
3a8pA02	6.10.140.680	Special › Helix non-globular › Helix Hairpins ›	0.52	33.0	3.81e-01	95.6%	89.5%
3l09A01	1.20.58.1460	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.51	30.0	3.64e-01	83.6%	91.8%
6srbA02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.50	30.0	3.55e-01	82.4%	86.2%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1821876	4969.1.1.1 ↗	alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B	0.90	75.0	6.82e-01	86.2%	99.5%
3480544	4969.1.1.0 ↗	alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I	0.67	56.0	5.54e-01	87.4%	99.4%
3742213	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.59	39.0	3.74e-01	95.6%	57.3%
3611383	604.6.1.0 ↗	alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain	0.55	32.0	3.72e-01	79.2%	80.0%
3399487	109.3.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat	0.54	37.0	4.03e-01	82.4%	83.7%
3970386	601.4.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains	0.52	30.0	3.24e-01	72.3%	64.4%
4244497	109.1.1.1 ↗	alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C	0.52	35.0	3.77e-01	84.3%	82.3%
3705066	1075.1.1.1 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane	0.52	45.0	3.90e-01	95.6%	72.7%
3180716	109.1.1.1 ↗	alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C	0.50	34.0	3.67e-01	84.3%	80.0%
3794988	604.6.1.0 ↗	alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain	0.50	30.0	3.36e-01	78.6%	74.4%

D3 medium residues 30-83

PDB

Domain cluster: representative

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4844112	1058.1.1.1 ↗	extended segments › Herpes DNA polymerase N-terminal domain › Herpes DNA polymerase N-terminal domain › Herpes DNA polymerase N-terminal domain › PF31254	0.89	82.0	7.13e-01	100.0%	75.6%
2732224	1058.1.1.1 ↗	extended segments › Herpes DNA polymerase N-terminal domain › Herpes DNA polymerase N-terminal domain › Herpes DNA polymerase N-terminal domain › PF31254	0.88	81.0	7.01e-01	100.0%	74.7%

D4 medium residues 142-304

PDB

Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03104.26 best	DNA_pol_B_exo1	34.9	1.50e-08	39.9%	22.7%

D5 medium residues 619-648_755-874

PDB

Domain cluster: rep: NC_042352.1__YP_009639584.1__FGG68_gp42__00043__D422-604

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00136.27 best	DNA_pol_B	119.2	3.00e-34	80.7%	26.3%
PF00136.27	DNA_pol_B	46.2	4.30e-12	21.3%	6.8%

D6 medium residues 649-754

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	110.8	1.10e-31	100.0%	23.4%