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helicase

Euk-Vir

Cricetid_gammaherpesvirus_2

helicase__YP_004207880__Cricetid_gammaherpesvirus_2__1605972

Identity

Accession:: YP_004207880 ↗
Protein ID:: helicase
Kingdom:: euk

Quality

85.0 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Rhadinovirus› Cricetid_gammaherpesvirus_2

TaxID: 1605972

Cluster

View cluster (90 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 292-359_699-758

PDB

Domain cluster: rep: helicase-primase_ATPase_subunit__YP_010087484__Phascolarctid_gammaherpesvirus_1__2249313__D338-366_706-759

Pfam (3)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01443.25 best	Viral_helicase1	22.9	9.20e-05	75.8%	27.6%
PF02689.21	Herpes_Helicase	93.6	1.20e-26	53.1%	7.9%
PF02689.21	Herpes_Helicase	91.2	6.50e-26	49.2%	7.3%

D2 high residues 452-525_541-594

PDB

Domain cluster: rep: helicase-primase_helicase_subunit__YP_004940266__Saimiriine_betaherpesvirus_4__1535247__D509-572_638-677

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02689.21 best	Herpes_Helicase	61.3	7.00e-17	57.8%	8.5%
PF02689.21	Herpes_Helicase	29.0	4.00e-07	46.9%	6.8%

CATH (39)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1gvnA00	1.10.8.130	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.72	47.0	5.54e-01	70.3%	96.6%
2oqmB01	1.20.120.450	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain	0.71	53.0	4.85e-01	78.1%	100.0%
1w27A02	1.20.200.10	Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain)	0.68	60.0	4.31e-01	93.0%	92.2%
4jioA01	1.20.120.560	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › alix/aip1 in complex with the ypdl late domain	0.67	46.0	4.26e-01	70.3%	84.5%
2ot4A03	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.67	47.0	5.05e-01	71.9%	86.9%
5h5mA02	1.20.120.230	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like	0.67	54.0	5.40e-01	85.9%	97.7%
1z23A00	1.20.120.830	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Serine-rich domain	0.67	54.0	5.03e-01	87.5%	82.8%
1qdbA02	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.66	51.0	4.97e-01	82.0%	72.7%
6p73A02	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.66	51.0	4.98e-01	82.0%	74.8%
3qweA00	1.20.1270.60	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain	0.65	49.0	3.88e-01	78.1%	85.0%
1oahA02	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.65	51.0	4.95e-01	82.0%	80.3%
1fntc01	1.20.120.180	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain	0.65	53.0	4.65e-01	86.7%	79.3%
3wscA00	1.20.1420.20	Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › M75 peptidase, HXXE motif	0.65	55.0	4.43e-01	93.0%	79.7%
3o10C00	1.20.120.330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2	0.65	52.0	5.13e-01	85.2%	94.9%
3caxA01	1.20.120.520	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like	0.64	56.0	4.70e-01	95.3%	71.9%
1w0bA01	1.20.58.420	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP	0.63	34.0	3.95e-01	78.1%	71.7%
2q00B00	1.20.120.330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2	0.63	50.0	5.14e-01	84.4%	100.0%
3kavA00	1.20.1270.360	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ›	0.62	44.0	4.82e-01	78.1%	91.2%
1yo7A00	1.20.120.230	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like	0.62	47.0	4.81e-01	78.9%	87.5%
1x8zB00	1.20.140.40	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein	0.62	47.0	4.48e-01	79.7%	72.1%
1g4uS01	1.20.120.260	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain	0.62	51.0	5.17e-01	89.8%	90.6%
5d91A02	1.20.120.1760	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain	0.61	52.0	4.48e-01	91.4%	70.2%
3tdoA00	1.20.1080.10	Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein.	0.56	41.0	3.33e-01	77.3%	83.7%
1cf7B00	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	0.56	35.0	4.25e-01	95.3%	98.8%
5lx8A00	1.25.40.390	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.56	45.0	2.95e-01	85.2%	45.7%
5wp3B00	1.10.132.20	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor	0.55	37.0	4.07e-01	71.1%	84.3%
1wdhA02	1.10.720.60	Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 ›	0.55	37.0	4.11e-01	96.1%	85.3%
3ddeB00	1.20.910.10	Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like	0.55	46.0	3.91e-01	94.5%	88.3%
4an8A02	1.10.132.100	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 ›	0.55	41.0	4.18e-01	77.3%	91.8%
1f6fA00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.54	44.0	3.97e-01	88.3%	83.6%
4ceiA03	6.10.250.2380	Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.54	38.0	4.08e-01	80.5%	84.8%
4mhlA00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.53	44.0	4.07e-01	88.3%	88.8%
4rajA00	1.20.910.10	Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like	0.53	46.0	3.90e-01	96.1%	93.1%
5nl6B01	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.53	37.0	3.83e-01	71.9%	90.9%
1tdzA02	1.10.8.50	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.52	36.0	3.59e-01	83.6%	67.2%
1hciA03	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.51	36.0	3.79e-01	72.7%	91.7%
4gc0A02	1.20.1250.20	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains	0.51	43.0	3.60e-01	93.0%	64.6%
1kqfC00	1.20.950.20	Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C	0.51	42.0	3.60e-01	92.2%	77.3%
1dvgA00	1.20.910.10	Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like	0.50	42.0	3.64e-01	94.5%	92.1%

ECOD (30)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3839810	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	0.69	49.0	4.79e-01	72.7%	79.3%
3227678	632.1.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain	0.69	47.0	5.31e-01	70.3%	90.0%
3273600	601.20.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Apolipophorin-III › Apolipophorin-III	0.65	57.0	4.75e-01	96.1%	75.6%
4967507	601.7.1.2 ↗	alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN	0.65	55.0	5.31e-01	91.4%	93.8%
3455183	611.7.1.11 ↗	alpha bundles › N-cbl like › Mixed lineage kinase domain-like (MLKL) N-terminal domain › Mixed lineage kinase domain-like (MLKL) N-terminal domain › DUF7032	0.64	43.0	4.14e-01	71.1%	59.3%
3309328	601.14.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin	0.62	54.0	4.43e-01	96.1%	64.6%
4025954	3758.1.1.0 ↗	alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins	0.61	50.0	4.04e-01	89.1%	89.6%
4996991	3883.1.1.1 ↗	alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf	0.61	50.0	4.27e-01	90.6%	61.4%
5026368	1075.1.1.67 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › 12TM_1	0.59	41.0	3.32e-01	71.1%	86.0%
3712159	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.59	44.0	4.17e-01	78.9%	69.0%
3653751	5058.1.1.11 ↗	alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › TerC	0.58	44.0	3.64e-01	79.7%	96.5%
4214015	101.11.1.0 ↗	alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	0.56	31.0	3.34e-01	78.9%	61.8%
3164482	5050.1.1.9 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1	0.55	46.0	4.02e-01	91.4%	67.5%
4631214	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.55	41.0	3.79e-01	78.1%	69.4%
3951281	109.3.1.160 ↗	alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › EccD	0.55	46.0	4.05e-01	92.2%	96.4%
3908020	633.21.1.0 ↗	alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107	0.54	41.0	4.08e-01	80.5%	80.7%
2756826	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.53	31.0	3.28e-01	90.6%	63.5%
3503335	604.1.1.124 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_6	0.53	37.0	3.91e-01	71.9%	95.7%
3957915	5050.1.1.9 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1	0.52	41.0	3.67e-01	81.2%	84.0%
4021717	604.6.1.15 ↗	alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › Helo_like_N	0.52	41.0	3.80e-01	81.2%	94.2%
3766092	150.1.1.79 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Piezo_TM1-24	0.52	39.0	3.68e-01	78.9%	84.5%
3974312	5050.1.1.9 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1	0.52	43.0	3.78e-01	91.4%	72.3%
3704526	604.5.1.0 ↗	alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895)	0.51	37.0	3.42e-01	75.0%	85.5%
3466971	5050.1.1.2 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › PTR2	0.51	43.0	3.52e-01	93.0%	72.8%
3334905	3745.1.1.1 ↗	alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex	0.51	44.0	3.22e-01	97.7%	85.2%
3881402	5059.1.1.1 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA	0.51	40.0	3.02e-01	82.8%	74.5%
4929352	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	0.51	43.0	3.72e-01	93.8%	68.8%
5068364	5059.1.1.1 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA	0.51	42.0	3.18e-01	89.1%	42.1%
3264566	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	0.51	45.0	3.81e-01	96.9%	74.3%
3802077	3745.1.1.1 ↗	alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex	0.50	45.0	3.26e-01	98.4%	86.7%

D3 medium residues 38-60_138-183

PDB

Domain cluster: representative

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2wuiA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.52	34.0	2.51e-01	75.4%	22.0%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4013782	149.1.1.1 ↗	alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450	0.50	39.0	2.70e-01	88.4%	70.2%

D4 medium residues 61-137_184-291_759-779

PDB

Domain cluster: rep: ORF35__NP_733888__Callitrichine_gammaherpesvirus_3__106331__D45-78_114-298

Pfam (3)

Accession	Name	Score	E-value	Q cov	HMM cov
PF13401.13 best	AAA_22	27.3	5.40e-06	65.5%	76.1%
PF02689.21	Herpes_Helicase	197.1	6.30e-58	58.7%	13.7%
PF02689.21	Herpes_Helicase	107.9	5.70e-31	38.8%	10.3%

D5 medium residues 373-451

PDB

Domain cluster: rep: helicase-primase_helicase_subunit__NP_045354__Bovine_alphaherpesvirus_1__10320__D392-469_736-760

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02689.21 best	Herpes_Helicase	82.7	2.30e-23	100.0%	10.0%