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helicase-primase_subunit
Euk-VirTestudinid_alphaherpesvirus_3
helicase-primase_subunit__YP_009176932__Testudinid_alphaherpesvirus_3__2560801
Identity
- Accession:
- YP_009176932 ↗
- Protein ID:
- helicase-primase_subunit
- Kingdom:
- euk
Quality
69.2
mean pLDDT
Taxonomy
Heunggongvirae›
Peploviricota›
Herviviricetes›
Herpesvirales›
Orthoherpesviridae›
Scutavirus›
Testudinid_alphaherpesvirus_3
TaxID: 2560801
Cluster
View cluster (61 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 1-145
Domain cluster:
rep: helicase-primase_subunit__YP_004940263__Saimiriine_betaherpesvirus_4__1535247__D1-152
CATH (15)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2cqaA01 | 2.40.50.360 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain | 0.71 | 37.0 | 5.11e-01 | 95.9% | 100.0% |
| 1iz6A01 | 2.30.30.30 | Mainly Beta › Roll › SH3 type barrels. › | 0.68 | 27.0 | 3.72e-01 | 92.4% | 72.5% |
| 6s8zA01 | 2.30.30.30 | Mainly Beta › Roll › SH3 type barrels. › | 0.67 | 26.0 | 3.77e-01 | 92.4% | 79.0% |
| 3kojB00 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.65 | 39.0 | 4.91e-01 | 95.2% | 96.7% |
| 5l37C00 | 2.40.50.220 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › EutN/Ccml | 0.63 | 35.0 | 4.41e-01 | 93.1% | 91.9% |
| 1fguB01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.61 | 40.0 | 4.63e-01 | 94.5% | 90.5% |
| 4htgA03 | 3.30.160.40 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain | 0.60 | 26.0 | 3.40e-01 | 72.4% | 70.9% |
| 4qclA01 | 2.40.50.730 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.60 | 36.0 | 4.56e-01 | 98.6% | 100.0% |
| 2rsxA00 | 3.10.450.420 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.60 | 28.0 | 2.79e-01 | 92.4% | 39.6% |
| 4nspA00 | 3.30.2170.10 | Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily | 0.59 | 32.0 | 2.75e-01 | 91.7% | 30.7% |
| 1kk1A02 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.54 | 28.0 | 3.17e-01 | 71.7% | 64.0% |
| 3mswA00 | 2.40.128.720 | Mainly Beta › Beta Barrel › Lipocalin › | 0.53 | 26.0 | 2.66e-01 | 86.2% | 44.6% |
| 2rs7A01 | 3.30.160.20 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › | 0.52 | 25.0 | 3.32e-01 | 89.0% | 86.5% |
| 3ecrB03 | 3.30.160.40 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain | 0.50 | 29.0 | 3.41e-01 | 92.4% | 80.4% |
| 3e99A00 | 3.10.450.50 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.50 | 27.0 | 2.73e-01 | 89.0% | 48.6% |
ECOD (29)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 174115 | 2.1.1.6 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB | 0.66 | 39.0 | 5.01e-01 | 94.5% | 100.0% |
| 3822461 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.66 | 39.0 | 5.03e-01 | 96.6% | 100.0% |
| 5036293 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.65 | 40.0 | 4.74e-01 | 98.6% | 89.0% |
| 3957994 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.65 | 34.0 | 2.94e-01 | 75.2% | 33.5% |
| 5069068 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.65 | 38.0 | 4.67e-01 | 95.2% | 90.4% |
| 3924626 | 2484.1.1.4 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H | 0.65 | 31.0 | 3.87e-01 | 91.7% | 74.1% |
| 3598854 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.64 | 38.0 | 3.93e-01 | 94.5% | 60.7% |
| 3326860 | 2484.1.1.67 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 | 0.64 | 31.0 | 3.94e-01 | 92.4% | 77.6% |
| 3279407 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.64 | 40.0 | 4.53e-01 | 100.0% | 82.7% |
| 2579126 | 2.1.1.1 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosom_S12_S23 | 0.63 | 38.0 | 3.86e-01 | 94.5% | 59.7% |
| 5028505 | 2.1.1.1 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosom_S12_S23 | 0.63 | 38.0 | 3.90e-01 | 94.5% | 61.4% |
| 5001168 | 2.1.1.1 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosom_S12_S23 | 0.62 | 38.0 | 4.43e-01 | 94.5% | 86.0% |
| 3311932 | 2484.1.1.67 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 | 0.62 | 31.0 | 4.08e-01 | 91.0% | 89.3% |
| 5037301 | 2.1.1.111 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ssb-like_OB | 0.62 | 36.0 | 4.44e-01 | 93.8% | 89.4% |
| 3603237 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.62 | 39.0 | 4.54e-01 | 97.2% | 87.6% |
| 4135153 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.61 | 27.0 | 3.62e-01 | 87.6% | 77.3% |
| 3852952 | 330.1.1.5 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM | 0.61 | 31.0 | 3.99e-01 | 90.3% | 86.3% |
| 4512226 | 330.6.1.0 ↗ | a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 0.61 | 28.0 | 3.23e-01 | 89.0% | 58.1% |
| 184919 | 243.1.1.31 ↗ | a+b two layers › Cystatin-like › NTF2-like › NTF2-like › Endopep_inhib | 0.60 | 28.0 | 2.79e-01 | 92.4% | 39.6% |
| 4009147 | 2.1.1.292 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF30365 | 0.58 | 41.0 | 3.44e-01 | 98.6% | 42.9% |
| 4416182 | 241.15.1.3 ↗ | a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 | 0.58 | 32.0 | 3.68e-01 | 90.3% | 72.4% |
| 4646070 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.58 | 42.0 | 4.79e-01 | 100.0% | 99.1% |
| 3603056 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.58 | 27.0 | 3.59e-01 | 87.6% | 82.7% |
| 3670182 | 2.1.1.1 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosom_S12_S23 | 0.58 | 32.0 | 3.45e-01 | 87.6% | 62.4% |
| 3917054 | 241.15.1.3 ↗ | a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 | 0.57 | 31.0 | 3.34e-01 | 89.7% | 58.4% |
| 4048220 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.55 | 28.0 | 3.54e-01 | 92.4% | 83.7% |
| 4058654 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.55 | 29.0 | 3.43e-01 | 93.8% | 71.7% |
| 3194095 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.54 | 29.0 | 3.48e-01 | 93.1% | 76.8% |
| 3499841 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.53 | 27.0 | 3.33e-01 | 91.0% | 76.7% |
D2
medium
residues 146-348
Domain cluster:
rep: ORF31__NP_733884__Callitrichine_gammaherpesvirus_3__106331__D132-145_190-351
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03324.21 best | Herpes_HEPA | 65.1 | 8.80e-18 | 45.8% | 97.8% |
CATH (3)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 7cr6D01 | 3.100.10.20 | Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain | 0.52 | 22.0 | 3.34e-01 | 97.0% | 93.9% |
| 1a15A00 | 2.40.50.40 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.51 | 15.0 | 2.47e-01 | 83.3% | 67.2% |
| 1yqeA02 | 3.40.50.10700 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › AF0625-like | 0.51 | 25.0 | 3.53e-01 | 91.1% | 97.9% |
ECOD (3)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3514938 | 213.1.1.6 ↗ | a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › ODC_AZ | 0.55 | 24.0 | 2.97e-01 | 71.9% | 62.5% |
| 3619240 | 304.48.1.59 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_exo1, DNA_pol_B_exo2 | 0.52 | 48.0 | 3.26e-01 | 100.0% | 30.0% |
| 4363388 | 513.1.1.1 ↗ | a+b two layers › Obg GTP-binding protein C-terminal domain-like › Obg GTP-binding protein C-terminal domain › Obg GTP-binding protein C-terminal domain › DUF1967 | 0.50 | 25.0 | 3.35e-01 | 71.9% | 90.9% |
D3
medium
residues 349-548
Domain cluster:
rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
D4
medium
residues 549-622
Domain cluster:
representative
CATH (17)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3mvcB00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.66 | 50.0 | 4.02e-01 | 83.8% | 84.4% |
| 3axjB02 | 1.20.58.200 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 | 0.64 | 44.0 | 4.23e-01 | 73.0% | 62.4% |
| 1zoyD00 | 1.20.1300.10 | Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit | 0.64 | 54.0 | 4.92e-01 | 95.9% | 84.3% |
| 4uurA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.62 | 50.0 | 4.28e-01 | 89.2% | 88.7% |
| 7wboA01 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.62 | 45.0 | 3.45e-01 | 78.4% | 33.9% |
| 6q9jB02 | 1.20.1440.230 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain | 0.62 | 42.0 | 4.03e-01 | 71.6% | 98.9% |
| 4fxdA06 | 1.10.132.60 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain | 0.61 | 54.0 | 4.20e-01 | 97.3% | 79.4% |
| 3anwB00 | 1.20.58.2050 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.60 | 52.0 | 4.11e-01 | 100.0% | 85.8% |
| 6fhpD00 | 1.10.390.10 | Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 | 0.59 | 38.0 | 4.13e-01 | 77.0% | 79.0% |
| 4qclA05 | 1.10.132.60 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain | 0.59 | 53.0 | 4.08e-01 | 100.0% | 80.4% |
| 7yh2B01 | 3.30.1380.20 | Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 | 0.59 | 41.0 | 3.31e-01 | 74.3% | 46.7% |
| 1zylA03 | 1.20.1270.170 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.57 | 39.0 | 3.47e-01 | 70.3% | 67.0% |
| 5xfaA04 | 1.20.1440.230 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain | 0.56 | 41.0 | 4.00e-01 | 100.0% | 70.6% |
| 2vixA03 | 1.20.1280.240 | Mainly Alpha › Up-down Bundle › Monooxygenase › | 0.55 | 44.0 | 3.92e-01 | 89.2% | 91.2% |
| 1g41A01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.53 | 41.0 | 3.12e-01 | 98.6% | 33.2% |
| 3qybA02 | 1.10.8.270 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › putative rabgap domain of human tbc1 domain family member 14 like domains | 0.53 | 37.0 | 3.44e-01 | 73.0% | 73.1% |
| 2wyoC01 | 3.30.1490.250 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › | 0.53 | 38.0 | 3.46e-01 | 78.4% | 78.8% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3331809 | 375.1.9.23 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › Sterile | 0.82 | 56.0 | 4.12e-01 | 70.3% | 30.9% |
| 5001282 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.80 | 55.0 | 4.35e-01 | 71.6% | 77.2% |
| 5073213 | 2484.1.1.302 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB | 0.76 | 54.0 | 3.80e-01 | 74.3% | 55.9% |
| 4117026 | 5069.1.1.56 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › PF27518 | 0.75 | 57.0 | 3.99e-01 | 81.1% | 37.4% |
| 3718788 | 138.1.1.0 ↗ | alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain | 0.70 | 52.0 | 4.39e-01 | 91.9% | 47.2% |
| 3761289 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.67 | 57.0 | 4.66e-01 | 95.9% | 70.7% |
| 4993995 | 5069.1.1.15 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm | 0.66 | 49.0 | 4.00e-01 | 79.7% | 63.6% |
| 4600429 | 5069.1.3.1 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › Sdh_cyt | 0.66 | 55.0 | 4.67e-01 | 91.9% | 81.7% |
| 5042943 | 2007.1.3.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like | 0.64 | 54.0 | 4.06e-01 | 94.6% | 89.2% |
| 5047626 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.62 | 52.0 | 4.33e-01 | 90.5% | 71.2% |
| 4992050 | 5069.1.3.0 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits | 0.62 | 54.0 | 4.64e-01 | 94.6% | 97.4% |
| 4486707 | 103.4.1.5 ↗ | alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › KIX_2 | 0.61 | 42.0 | 4.06e-01 | 71.6% | 78.8% |
| 4947454 | 2002.1.1.0 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels | 0.58 | 43.0 | 2.95e-01 | 83.8% | 63.9% |
| 3277945 | 10.12.1.75 ↗ | beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding_2 | 0.56 | 46.0 | 3.39e-01 | 90.5% | 71.0% |
| 3981020 | 2007.5.1.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL | 0.55 | 44.0 | 2.95e-01 | 91.9% | 28.8% |
| 3602838 | 101.1.8.0 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes | 0.53 | 42.0 | 3.49e-01 | 89.2% | 60.0% |
| 3856583 | 604.12.1.2 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 | 0.52 | 41.0 | 3.90e-01 | 91.9% | 72.2% |