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DNA_packaging_terminase_subunit_2
Euk-VirWood_mouse_herpesvirus
DNA_packaging_terminase_subunit_2__YP_010085884__Wood_mouse_herpesvirus__432370
Identity
- Accession:
- YP_010085884 ↗
- Protein ID:
- DNA_packaging_terminase_subunit_2
- Kingdom:
- euk
Quality
77.2
mean pLDDT
Taxonomy
Heunggongvirae›
Peploviricota›
Herviviricetes›
Herpesvirales›
Orthoherpesviridae›
Rhadinovirus›
Wood_mouse_herpesvirus
TaxID: 432370
Cluster
View cluster (77 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
medium
residues 1-106_150-163
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 | 45.4 | 4.80e-12 | 80.0% | 12.8% |
D2
medium
residues 315-346_400-431
Domain cluster:
representative
CATH (19)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4v1gA00 | 1.20.20.10 | Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C | 0.70 | 56.0 | 5.16e-01 | 90.6% | 81.2% |
| 2x2vA00 | 1.20.20.10 | Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C | 0.69 | 57.0 | 5.68e-01 | 92.2% | 98.5% |
| 2kg7B00 | 1.10.287.1060 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like | 0.68 | 57.0 | 4.96e-01 | 92.2% | 70.1% |
| 3beyD00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.68 | 48.0 | 4.21e-01 | 73.4% | 52.1% |
| 1pd3A00 | 1.10.287.230 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.67 | 52.0 | 5.60e-01 | 90.6% | 98.1% |
| 6tkvA01 | 1.10.287.1060 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like | 0.65 | 57.0 | 5.60e-01 | 98.4% | 97.1% |
| 3ehfD01 | 1.20.5.1930 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.64 | 53.0 | 5.37e-01 | 90.6% | 98.4% |
| 6z01B03 | 1.10.132.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › | 0.63 | 49.0 | 3.70e-01 | 95.3% | 34.4% |
| 1ydxA02 | 1.10.287.1120 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein | 0.61 | 53.0 | 4.69e-01 | 95.3% | 96.7% |
| 6h9xA01 | 1.10.287.40 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain | 0.61 | 51.0 | 4.40e-01 | 93.8% | 75.5% |
| 2q0oC00 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.60 | 53.0 | 4.84e-01 | 98.4% | 76.7% |
| 2bdeA03 | 1.20.58.1160 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.60 | 52.0 | 4.96e-01 | 98.4% | 89.6% |
| 1gvnA00 | 1.10.8.130 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › | 0.59 | 49.0 | 4.43e-01 | 90.6% | 70.1% |
| 1a36A04 | 1.10.132.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › | 0.59 | 50.0 | 3.67e-01 | 95.3% | 37.1% |
| 2ic6A00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 51.0 | 4.95e-01 | 95.3% | 91.5% |
| 5mmjo00 | 1.10.287.10 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding | 0.58 | 47.0 | 4.46e-01 | 98.4% | 74.7% |
| 3txsC01 | 1.10.287.1060 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like | 0.57 | 47.0 | 4.54e-01 | 100.0% | 80.0% |
| 6qs7C01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.57 | 47.0 | 3.66e-01 | 95.3% | 43.2% |
| 2ekgB01 | 6.10.250.3270 | Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.57 | 41.0 | 4.29e-01 | 76.6% | 92.9% |
ECOD (7)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3354385 | 3755.1.1.22 ↗ | alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › DUF3475 | 0.63 | 54.0 | 3.80e-01 | 96.9% | 37.6% |
| 4315986 | 192.7.1.2 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N | 0.62 | 52.0 | 4.60e-01 | 90.6% | 81.1% |
| 3249654 | 604.5.1.32 ↗ | alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › TMEM120A-B | 0.60 | 55.0 | 5.07e-01 | 100.0% | 97.5% |
| 4613294 | 4177.1.1.22 ↗ | alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › LXG | 0.58 | 46.0 | 3.35e-01 | 93.8% | 70.2% |
| 3943105 | 2004.1.1.5 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran | 0.58 | 46.0 | 2.75e-01 | 93.8% | 10.9% |
| 3882466 | 192.7.1.0 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm | 0.55 | 48.0 | 3.99e-01 | 98.4% | 73.9% |
| 2482296 | 192.7.1.2 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N | 0.54 | 48.0 | 4.04e-01 | 100.0% | 57.3% |
D3
medium
residues 461-483_571-651
Domain cluster:
representative
CATH (11)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3vkhB07 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.66 | 50.0 | 4.12e-01 | 79.8% | 96.8% |
| 4h63Q04 | 3.90.1150.120 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › | 0.66 | 49.0 | 4.75e-01 | 77.9% | 86.2% |
| 4ndoA00 | 3.40.1160.10 | Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like | 0.61 | 44.0 | 3.35e-01 | 75.0% | 84.5% |
| 1in4A01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.56 | 43.0 | 3.84e-01 | 82.7% | 85.9% |
| 4e5nC01 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.56 | 41.0 | 3.78e-01 | 76.9% | 85.0% |
| 2r0qC02 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.55 | 20.0 | 2.63e-01 | 89.4% | 54.5% |
| 2ykgA01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.53 | 43.0 | 3.41e-01 | 87.5% | 76.9% |
| 2prsA02 | 3.40.50.1980 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain | 0.52 | 37.0 | 3.68e-01 | 75.0% | 90.4% |
| 3by4A00 | 3.90.70.80 | Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › | 0.52 | 47.0 | 3.92e-01 | 98.1% | 70.3% |
| 1xdzA00 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.51 | 39.0 | 3.12e-01 | 84.6% | 86.6% |
| 1l1qA00 | 3.40.50.2020 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.50 | 38.0 | 3.25e-01 | 81.7% | 76.2% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3061396 | 192.6.1.3 ↗ | alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATPD_C_metazoa | 0.61 | 24.0 | 3.50e-01 | 93.3% | 80.4% |
| 4969391 | 2007.1.5.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like | 0.54 | 46.0 | 4.08e-01 | 99.0% | 96.9% |
| 1165753 | 219.1.1.15 ↗ | a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU | 0.51 | 47.0 | 3.88e-01 | 98.1% | 69.1% |
| 3488054 | 207.1.1.22 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6 | 0.50 | 39.0 | 2.99e-01 | 82.7% | 41.6% |