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DNA_packaging_terminase_subunit_2

Euk-Vir

Ateline_alphaherpesvirus_1

DNA_packaging_terminase_subunit_2__YP_009361909__Ateline_alphaherpesvirus_1__35243

Identity

Accession:: YP_009361909 ↗
Protein ID:: DNA_packaging_terminase_subunit_2
Kingdom:: euk

Quality

78.7 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Simplexvirus› Ateline_alphaherpesvirus_1

TaxID: 35243

Cluster

View cluster (77 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 medium residues 28-144

PDB

Domain cluster: rep: transport_protein__YP_004207847__Cricetid_gammaherpesvirus_2__1605972__D1-97

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	86.7	1.50e-24	99.2%	16.8%

D2 medium residues 255-290_357-380

PDB

Domain cluster: representative

CATH (29)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2gfhA02	1.20.120.710	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain	0.73	62.0	5.53e-01	95.0%	72.1%
8igrI01	2.40.270.10	Mainly Beta › Beta Barrel › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 › DNA-directed RNA polymerase, subunit 2, domain 6	0.72	50.0	3.56e-01	73.3%	27.3%
1c9bA02	1.10.472.10	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like	0.69	60.0	4.92e-01	95.0%	58.5%
2z15A00	3.90.640.90	Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › Anti-proliferative protein, N-terminal domain	0.68	59.0	4.71e-01	96.7%	63.9%
4rocA01	1.10.472.10	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like	0.68	58.0	4.91e-01	98.3%	67.0%
1c9bA01	1.10.472.10	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like	0.67	59.0	5.02e-01	98.3%	67.0%
3h4cA01	1.10.472.10	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like	0.66	57.0	4.88e-01	96.7%	69.8%
2okuA00	1.20.120.470	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Acyl-CoA dehydrogenase, C-terminal domain	0.65	57.0	4.56e-01	98.3%	77.0%
4nlbA02	1.10.150.80	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain	0.65	56.0	4.81e-01	95.0%	71.3%
2no4A02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.65	54.0	5.09e-01	95.0%	85.3%
1cpyA02	1.10.287.410	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.64	52.0	4.99e-01	95.0%	97.2%
3fblA00	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.61	49.0	4.53e-01	93.3%	79.3%
2px0A01	1.20.120.1380	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar FlhF biosynthesis protein, N domain	0.61	52.0	4.96e-01	98.3%	87.7%
3fvvA02	1.20.1440.100	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › SG protein - dephosphorylation function	0.61	48.0	4.53e-01	100.0%	70.7%
3k7dA03	1.20.120.330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2	0.60	52.0	3.97e-01	95.0%	50.0%
6rxaA01	1.10.40.30	Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain)	0.60	52.0	4.60e-01	98.3%	71.3%
4m70I00	1.20.5.4130	Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.59	51.0	4.27e-01	100.0%	83.3%
3t46A00	1.20.1270.10	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ›	0.58	50.0	4.61e-01	93.3%	80.0%
1xvhB00	1.20.120.1850	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Ebh helix bundles repeating unit (S and A modules)	0.58	46.0	3.86e-01	95.0%	54.2%
6jkvA00	3.60.40.10	Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain	0.58	46.0	3.24e-01	96.7%	56.1%
2vo9A01	3.30.1380.10	Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 ›	0.58	49.0	3.85e-01	96.7%	95.5%
1qgtB00	1.10.4090.10	Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus	0.56	47.0	3.68e-01	100.0%	65.0%
3ctwB00	1.10.8.930	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Protein of unknown function DUF1465	0.56	44.0	3.54e-01	86.7%	74.2%
5egwA00	3.90.70.10	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases	0.55	49.0	3.05e-01	100.0%	80.7%
4unfA02	1.10.340.30	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2	0.55	45.0	3.74e-01	95.0%	86.3%
3k1rA01	1.20.1160.20	Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) ›	0.54	47.0	4.28e-01	98.3%	96.3%
3hx3A01	1.10.8.20	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p	0.52	43.0	4.22e-01	96.7%	94.0%
1gs0A01	1.20.142.10	Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › Poly(ADP-ribose) polymerase, regulatory domain	0.51	41.0	3.18e-01	86.7%	47.3%
1mg7A01	3.30.70.1000	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Switch protein XOL-1, GHMP-like	0.51	43.0	3.17e-01	100.0%	58.3%

ECOD (24)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5043732	4009.1.1.0 ↗	alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins	0.76	68.0	6.44e-01	98.3%	88.6%
4034226	632.19.1.3 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542	0.75	65.0	5.87e-01	95.0%	87.5%
3930038	148.1.3.0 ↗	alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain	0.68	59.0	5.23e-01	100.0%	80.0%
5076381	101.1.10.3 ↗	alpha arrays › HTH › HTH › Cyclin-like › TFIIB	0.67	58.0	4.95e-01	98.3%	66.0%
4032748	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	0.66	57.0	3.99e-01	100.0%	41.5%
3942326	191.1.1.48 ↗	alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_46	0.66	54.0	4.26e-01	95.0%	77.0%
3337428	7579.1.1.5 ↗	a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S10	0.65	55.0	3.68e-01	100.0%	25.4%
2741727	101.1.10.14 ↗	alpha arrays › HTH › HTH › Cyclin-like › Cyclin_C_2	0.65	55.0	5.15e-01	98.3%	88.2%
5007277	632.11.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like	0.64	54.0	4.78e-01	93.3%	78.8%
5043394	632.11.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like	0.63	53.0	4.81e-01	91.7%	85.0%
4997861	4953.1.1.4 ↗	beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › ASL_C2	0.63	54.0	4.64e-01	95.0%	63.2%
4938672	632.11.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like	0.63	51.0	4.88e-01	91.7%	84.3%
5022856	7014.1.1.1 ↗	alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA	0.61	41.0	3.28e-01	76.7%	33.9%
3583897	148.1.3.0 ↗	alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain	0.60	49.0	4.67e-01	93.3%	75.7%
3979768	633.12.1.0 ↗	alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like	0.59	49.0	4.18e-01	93.3%	100.0%
4077186	632.15.1.4 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › HSP70	0.58	47.0	4.24e-01	91.7%	68.2%
3684979	192.3.1.0 ↗	alpha bundles › Long alpha-hairpin › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Fe,Mn superoxide dismutase (SOD), N-terminal domain	0.58	47.0	4.07e-01	91.7%	95.8%
3186781	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	0.56	48.0	3.26e-01	100.0%	68.8%
4223710	3054.1.1.0 ↗	alpha arrays › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol	0.54	47.0	3.93e-01	100.0%	57.3%
4028248	5059.1.1.1 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA	0.54	46.0	2.99e-01	98.3%	67.0%
3488339	601.1.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin	0.53	41.0	3.79e-01	93.3%	90.6%
3260787	143.1.1.1 ↗	alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain › PABP	0.52	41.0	3.94e-01	95.0%	96.0%
3958804	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	3.20e-01	100.0%	94.1%
1141813	159.1.2.2 ↗	alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG	0.50	39.0	3.34e-01	83.3%	91.5%

D3 medium residues 346-356_381-420

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	30.9	1.20e-07	100.0%	6.1%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5hayA02	1.25.40.440	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain	0.63	38.0	3.31e-01	100.0%	39.2%
1wjzA00	1.10.287.110	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain	0.52	35.0	2.92e-01	100.0%	38.3%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3968484	605.1.1.1 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA	0.55	37.0	3.40e-01	100.0%	51.4%
3601902	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	0.53	42.0	3.04e-01	100.0%	53.0%

D4 medium residues 421-454_508-560

PDB

Domain cluster: rep: DNA_packaging_terminase_subunit_2__NP_851888__Macacine_alphaherpesvirus_1__10325__D398-429_497-533

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	56.7	1.80e-15	64.4%	7.6%

D5 medium residues 561-586_613-733

PDB

Domain cluster: rep: orf7__YP_009044394__Alcelaphine_gammaherpesvirus_2__138184__D511-616

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	122.9	1.70e-35	63.9%	13.4%

D6 medium residues 587-612_734-809

PDB

Domain cluster: rep: terminase_subunit_2__YP_009179297__Elephant_endotheliotropic_herpesvirus_4__548914__D513-536_648-697