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DNA_cleavage_packaging_protein
Euk-VirHawaiian_green_turtle_herpesvirus
DNA_cleavage_packaging_protein__YP_009207093__Hawaiian_green_turtle_herpesvirus__70564
Identity
- Accession:
- YP_009207093 ↗
- Protein ID:
- DNA_cleavage_packaging_protein
- Kingdom:
- euk
Quality
74.2
mean pLDDT
Taxonomy
Heunggongvirae›
Peploviricota›
Herviviricetes›
Herpesvirales›
Orthoherpesviridae›
Scutavirus›
Hawaiian_green_turtle_herpesvirus
TaxID: 70564
Cluster
View cluster (76 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
high
residues 1-103_380-397
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01673.24 best | Herpes_env | 93.3 | 2.50e-26 | 95.9% | 19.4% |
CATH (22)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4h3tA02 | 1.10.132.100 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › | 0.62 | 43.0 | 4.11e-01 | 71.1% | 95.0% |
| 1vw4L01 | 3.90.1030.10 | Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 | 0.62 | 40.0 | 3.94e-01 | 87.6% | 59.3% |
| 8sbeA02 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.62 | 44.0 | 3.81e-01 | 73.6% | 98.9% |
| 2gfhA02 | 1.20.120.710 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain | 0.56 | 35.0 | 4.00e-01 | 72.7% | 87.2% |
| 1aepA00 | 1.20.120.20 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein | 0.56 | 39.0 | 3.67e-01 | 71.9% | 71.9% |
| 3f4mA00 | 1.20.1440.160 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like | 0.55 | 49.0 | 4.59e-01 | 100.0% | 87.7% |
| 1hbgA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.55 | 39.0 | 3.71e-01 | 73.6% | 96.6% |
| 1a41A02 | 1.20.120.380 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 | 0.55 | 36.0 | 3.97e-01 | 76.9% | 84.0% |
| 4limA00 | 3.90.920.10 | Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain | 0.55 | 43.0 | 3.03e-01 | 83.5% | 61.4% |
| 5z7qA00 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.54 | 41.0 | 3.62e-01 | 79.3% | 85.8% |
| 3hdiA02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.54 | 39.0 | 3.31e-01 | 74.4% | 89.4% |
| 1oj6A00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.53 | 37.0 | 3.53e-01 | 72.7% | 96.6% |
| 1yhuB00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.53 | 40.0 | 3.83e-01 | 81.0% | 98.6% |
| 3hd6A00 | 1.10.3430.10 | Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains | 0.53 | 37.0 | 2.64e-01 | 73.6% | 65.3% |
| 1zcdA00 | 1.20.1530.10 | Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain | 0.53 | 41.0 | 2.90e-01 | 81.8% | 61.4% |
| 2rd3D00 | 1.20.910.10 | Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like | 0.52 | 37.0 | 3.17e-01 | 74.4% | 86.2% |
| 1binA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.52 | 39.0 | 3.72e-01 | 78.5% | 98.6% |
| 1hr6B02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.51 | 37.0 | 3.14e-01 | 74.4% | 95.2% |
| 1x9fD00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.51 | 38.0 | 3.69e-01 | 79.3% | 100.0% |
| 4mcwA02 | 1.10.3210.10 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 | 0.51 | 41.0 | 3.60e-01 | 89.3% | 99.0% |
| 2oifB00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.51 | 36.0 | 3.34e-01 | 72.7% | 79.5% |
| 5eufA01 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.50 | 36.0 | 3.03e-01 | 75.2% | 84.7% |
ECOD (20)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5048002 | 4953.1.1.0 ↗ | beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like | 0.72 | 54.0 | 5.17e-01 | 77.7% | 77.8% |
| 4527464 | 633.24.1.5 ↗ | alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › PF29080 | 0.66 | 46.0 | 5.13e-01 | 71.1% | 95.8% |
| 3645542 | 150.1.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin | 0.62 | 43.0 | 4.17e-01 | 70.2% | 100.0% |
| 4029516 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.60 | 44.0 | 3.90e-01 | 76.9% | 95.6% |
| 3261117 | 633.24.1.2 ↗ | alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › DUF5601 | 0.60 | 42.0 | 4.62e-01 | 71.1% | 93.7% |
| 3270794 | 609.1.1.1 ↗ | alpha bundles › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase › PARP_reg | 0.59 | 38.0 | 3.76e-01 | 71.1% | 60.8% |
| 3179160 | 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 | 0.57 | 42.0 | 3.58e-01 | 76.9% | 87.3% |
| 4857952 | 4963.1.2.1 ↗ | alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal domain in vesicular stomatitis virus RNA polymerase L › Mononeg_RNA_pol | 0.57 | 46.0 | 4.05e-01 | 87.6% | 66.5% |
| 3723579 | 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 | 0.55 | 40.0 | 3.26e-01 | 76.9% | 72.8% |
| 5001606 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.55 | 34.0 | 3.19e-01 | 76.9% | 51.7% |
| 4547108 | 2007.1.19.4 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › SAT | 0.54 | 39.0 | 2.95e-01 | 74.4% | 44.2% |
| 3974439 | 2002.1.1.4 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Alpha-amylase | 0.54 | 41.0 | 2.48e-01 | 80.2% | 14.1% |
| 3688033 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.53 | 42.0 | 3.69e-01 | 83.5% | 80.6% |
| 3799795 | 627.1.1.1 ↗ | alpha complex topology › VPS9 domain › VPS9 domain › VPS9 domain › VPS9 | 0.52 | 37.0 | 3.55e-01 | 75.2% | 92.7% |
| 3998525 | 196.1.1.1 ↗ | alpha bundles › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › RGS | 0.51 | 37.0 | 3.27e-01 | 75.2% | 54.4% |
| 4217297 | 192.29.1.123 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › UPF0093 | 0.51 | 38.0 | 3.58e-01 | 77.7% | 78.6% |
| 3244338 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.51 | 38.0 | 3.41e-01 | 79.3% | 90.2% |
| 3997392 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.51 | 37.0 | 3.32e-01 | 76.9% | 88.3% |
| 3613554 | 304.102.1.1 ↗ | a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_2 | 0.50 | 36.0 | 2.44e-01 | 98.3% | 19.6% |
| 3998222 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.50 | 37.0 | 3.48e-01 | 77.7% | 92.2% |
D2
medium
residues 170-190_275-379
Domain cluster:
rep: DNA_packaging_protein_UL32__YP_010084958__Beluga_whale_alphaherpesvirus_1__1434720__D379-511
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01673.24 best | Herpes_env | 113.9 | 1.40e-32 | 89.7% | 19.2% |
D3
medium
residues 191-274
D4
medium
residues 405-457
Domain cluster:
rep: DNA_packaging_protein_UL32__YP_009042094__Fruit_bat_alphaherpesvirus_1__1343901__D516-583
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01673.24 best | Herpes_env | 48.7 | 8.40e-13 | 100.0% | 10.0% |
CATH (29)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6xkyA01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.81 | 58.0 | 3.90e-01 | 75.5% | 95.7% |
| 4fvmA06 | 1.10.287.690 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain | 0.80 | 56.0 | 5.89e-01 | 75.5% | 81.2% |
| 4fxdA04 | 3.90.1600.10 | Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain | 0.80 | 56.0 | 3.97e-01 | 75.5% | 25.5% |
| 1zhcA00 | 6.10.280.50 | Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.79 | 56.0 | 4.97e-01 | 75.5% | 56.6% |
| 2a2cA03 | 1.20.1440.340 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.79 | 54.0 | 3.93e-01 | 73.6% | 27.5% |
| 7k3zG01 | 3.50.7.10 | Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL | 0.78 | 52.0 | 3.42e-01 | 71.7% | 17.4% |
| 4adnA01 | 1.20.1280.250 | Mainly Alpha › Up-down Bundle › Monooxygenase › | 0.77 | 69.0 | 5.85e-01 | 100.0% | 70.6% |
| 1x4tA01 | 1.10.287.660 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin | 0.76 | 55.0 | 5.35e-01 | 75.5% | 69.0% |
| 1ydxA02 | 1.10.287.1120 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein | 0.75 | 52.0 | 4.42e-01 | 73.6% | 82.2% |
| 3a8pA02 | 6.10.140.680 | Special › Helix non-globular › Helix Hairpins › | 0.74 | 56.0 | 4.42e-01 | 83.0% | 63.2% |
| 1yxrA01 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.73 | 61.0 | 5.45e-01 | 92.5% | 90.5% |
| 3zdmB00 | 1.20.5.420 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C | 0.73 | 54.0 | 5.57e-01 | 81.1% | 90.0% |
| 2a26B01 | 4.10.860.10 | Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain | 0.72 | 50.0 | 5.32e-01 | 75.5% | 90.9% |
| 1b04A03 | 1.10.287.610 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin | 0.70 | 56.0 | 5.35e-01 | 88.7% | 98.4% |
| 3g0oA02 | 1.10.1040.10 | Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 | 0.70 | 57.0 | 4.44e-01 | 92.5% | 81.8% |
| 2yevA02 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.68 | 48.0 | 4.39e-01 | 75.5% | 59.5% |
| 1nf1A01 | 1.10.506.10 | Mainly Alpha › Orthogonal Bundle › GTPase Activation - p120GAP; domain 1 › GTPase Activation - p120gap; domain 1 | 0.67 | 47.0 | 4.11e-01 | 75.5% | 48.2% |
| 6tkvA01 | 1.10.287.1060 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like | 0.67 | 46.0 | 4.31e-01 | 73.6% | 64.7% |
| 2hh7A00 | 1.20.58.1000 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer | 0.66 | 48.0 | 4.15e-01 | 77.4% | 84.7% |
| 3k2nA00 | 3.30.450.40 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain | 0.65 | 54.0 | 3.90e-01 | 100.0% | 94.4% |
| 2vx2G02 | 1.10.12.10 | Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 | 0.65 | 47.0 | 4.65e-01 | 75.5% | 76.4% |
| 4i43B02 | 3.30.43.40 | Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain | 0.65 | 53.0 | 4.34e-01 | 100.0% | 92.1% |
| 3ne5B04 | 6.10.140.730 | Special › Helix non-globular › Helix Hairpins › | 0.63 | 49.0 | 5.04e-01 | 100.0% | 94.1% |
| 4jylA02 | 1.10.12.10 | Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 | 0.63 | 44.0 | 4.58e-01 | 73.6% | 85.7% |
| 1zl8B00 | 1.10.287.650 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain | 0.62 | 43.0 | 4.30e-01 | 73.6% | 75.9% |
| 2wvxA04 | 1.20.1610.10 | Mainly Alpha › Up-down Bundle › Glycosyl hydrolase family fold › alpha-1,2-mannosidases domains | 0.60 | 46.0 | 3.34e-01 | 88.7% | 86.7% |
| 3sllA02 | 1.10.12.10 | Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 | 0.59 | 42.0 | 4.11e-01 | 79.2% | 73.8% |
| 7jiuA03 | 3.30.1010.10 | Alpha Beta › 2-Layer Sandwich › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 | 0.58 | 50.0 | 3.77e-01 | 100.0% | 76.5% |
| 5vjhB03 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.55 | 45.0 | 3.10e-01 | 96.2% | 65.3% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3965957 | 5086.1.1.84 ↗ | alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND | 0.80 | 55.0 | 4.96e-01 | 73.6% | 61.3% |
| 3879987 | 601.48.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain | 0.79 | 60.0 | 5.65e-01 | 86.8% | 67.7% |
| 4568335 | 3812.1.1.8 ↗ | alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › DUF5398 | 0.77 | 54.0 | 4.99e-01 | 75.5% | 58.0% |
| 2926 | 616.1.1.2 ↗ | alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › WHEP-TRS | 0.76 | 55.0 | 5.49e-01 | 77.4% | 90.7% |
| 5075979 | 159.1.2.0 ↗ | alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related | 0.73 | 54.0 | 5.12e-01 | 81.1% | 80.0% |
| 4975294 | 601.28.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like | 0.72 | 60.0 | 5.14e-01 | 98.1% | 83.3% |
| 3616186 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.72 | 62.0 | 3.76e-01 | 98.1% | 37.7% |
| 3682710 | 2004.1.1.529 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, DUF6469 | 0.65 | 57.0 | 3.35e-01 | 100.0% | 72.3% |