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VLF-1
Euk-VirHomarus_gammarus_nudivirus
VLF-1__YP_010087683__Homarus_gammarus_nudivirus__2509616
Identity
- Accession:
- YP_010087683 ↗
- Protein ID:
- VLF-1
- Kingdom:
- euk
Quality
73.2
mean pLDDT
Cluster
Singleton — not in a non-trivial cluster
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 2-88
D2
medium
residues 96-149_209-286
Domain cluster:
rep: INT__YP_009116690__Tipula_oleracea_nudivirus__1546257__D118-175_236-299
CATH (18)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1f44A01 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.79 | 67.0 | 5.79e-01 | 89.4% | 99.5% |
| 5jk0B01 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.75 | 60.0 | 5.41e-01 | 83.3% | 98.8% |
| 2v6eA03 | 1.10.443.30 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Telomere resolvase | 0.73 | 63.0 | 5.18e-01 | 90.9% | 92.4% |
| 2a3vA02 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.72 | 60.0 | 4.99e-01 | 86.4% | 96.7% |
| 3nkhA00 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.72 | 61.0 | 5.05e-01 | 89.4% | 93.7% |
| 1aihA00 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.71 | 60.0 | 5.47e-01 | 89.4% | 90.0% |
| 1ae9A00 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.69 | 52.0 | 4.71e-01 | 77.3% | 91.8% |
| 1floC02 | 1.10.443.10 | Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core | 0.64 | 55.0 | 4.32e-01 | 89.4% | 79.8% |
| 2om6A02 | 1.10.150.400 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › | 0.62 | 32.0 | 4.06e-01 | 84.8% | 83.5% |
| 5xdcB01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.60 | 35.0 | 3.77e-01 | 96.2% | 66.7% |
| 4ks9A01 | 1.20.140.90 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain | 0.59 | 31.0 | 3.24e-01 | 93.2% | 54.0% |
| 1ki1B01 | 1.20.900.10 | Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain | 0.56 | 40.0 | 3.54e-01 | 73.5% | 89.4% |
| 4fm3A00 | 1.20.1270.390 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.56 | 25.0 | 2.89e-01 | 86.4% | 54.7% |
| 8ciwB01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.53 | 33.0 | 3.51e-01 | 97.0% | 70.4% |
| 7ncyB01 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.53 | 31.0 | 3.23e-01 | 87.9% | 60.3% |
| 3bqoA00 | 1.25.40.210 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Telomere repeat-binding factor, dimerisation domain | 0.52 | 39.0 | 3.45e-01 | 79.5% | 68.8% |
| 3rrwB01 | 1.10.520.10 | Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › | 0.52 | 42.0 | 3.79e-01 | 87.1% | 97.8% |
| 2hoqA02 | 1.10.150.520 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › | 0.51 | 26.0 | 3.20e-01 | 76.5% | 78.5% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5059725 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.73 | 61.0 | 5.44e-01 | 87.9% | 92.2% |
| 4004483 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.72 | 61.0 | 5.34e-01 | 89.4% | 92.6% |
| 3964171 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.71 | 59.0 | 5.39e-01 | 87.9% | 94.8% |
| 4981966 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.71 | 60.0 | 5.15e-01 | 88.6% | 91.0% |
| 4182686 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.70 | 60.0 | 5.23e-01 | 90.2% | 97.4% |
| 4928148 | 101.1.8.0 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes | 0.70 | 55.0 | 5.09e-01 | 82.6% | 96.4% |
| 4940211 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.70 | 58.0 | 5.27e-01 | 86.4% | 100.0% |
| 5002702 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.70 | 59.0 | 5.21e-01 | 90.2% | 92.6% |
| 3925921 | 109.4.1.823 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Htt_N-HEAT_1 | 0.70 | 36.0 | 2.47e-01 | 100.0% | 15.4% |
| 4637388 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.69 | 58.0 | 5.32e-01 | 88.6% | 93.5% |
| 5028306 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.69 | 58.0 | 5.17e-01 | 87.9% | 95.0% |
| 3208241 | 101.1.8.10 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › DUF3435 | 0.63 | 57.0 | 4.40e-01 | 97.7% | 95.0% |
| 3990290 | 109.4.1.842 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARMC9_ARM | 0.59 | 31.0 | 2.66e-01 | 98.5% | 29.8% |
| 3569413 | 133.1.1.1 ↗ | alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF | 0.58 | 46.0 | 3.93e-01 | 84.1% | 91.6% |
| 3974221 | 601.4.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains | 0.54 | 33.0 | 3.38e-01 | 100.0% | 60.8% |
| 4507639 | 102.1.2.0 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase | 0.54 | 28.0 | 3.54e-01 | 93.9% | 85.3% |
| 3815745 | 592.6.1.1 ↗ | alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug | 0.54 | 30.0 | 3.77e-01 | 89.4% | 91.3% |
| 3973500 | 601.1.2.144 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › HBM | 0.52 | 33.0 | 3.48e-01 | 100.0% | 71.3% |
| 4474376 | 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 | 0.52 | 38.0 | 3.78e-01 | 99.2% | 74.1% |
D3
medium
residues 150-208
Domain cluster:
representative
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1a31A03 | 3.90.15.10 | Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 | 0.61 | 51.0 | 3.93e-01 | 100.0% | 45.3% |
| 2giaA00 | 2.30.31.40 | Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › | 0.60 | 43.0 | 3.27e-01 | 78.0% | 52.6% |
| 8dy9I01 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.57 | 43.0 | 3.04e-01 | 84.7% | 51.9% |
| 2kloA00 | 1.10.10.1420 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DNA replication factor Cdt1, C-terminal WH domain | 0.56 | 40.0 | 3.15e-01 | 79.7% | 66.7% |
| 2v1nA01 | 1.10.10.2030 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DNA/RNA-binding protein Kin17, conserved domain | 0.55 | 38.0 | 3.29e-01 | 74.6% | 83.2% |
| 3hyiA01 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.54 | 46.0 | 3.29e-01 | 100.0% | 78.0% |
| 1tbxB00 | 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 | 0.53 | 38.0 | 3.37e-01 | 76.3% | 85.6% |
| 3c0wA02 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.52 | 39.0 | 3.37e-01 | 84.7% | 83.5% |
| 3pqkA00 | 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 | 0.52 | 37.0 | 3.23e-01 | 79.7% | 74.7% |
| 1vq0A02 | 3.90.1280.10 | Alpha Beta › Alpha-Beta Complex › CBS domain Like › HSP33 redox switch-like | 0.51 | 34.0 | 3.50e-01 | 71.2% | 82.5% |
ECOD (15)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4410774 | 101.1.8.0 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes | 0.63 | 50.0 | 4.11e-01 | 100.0% | 46.1% |
| 4952765 | 101.1.8.1 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase | 0.62 | 52.0 | 4.09e-01 | 100.0% | 45.0% |
| 3403298 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.62 | 45.0 | 3.43e-01 | 78.0% | 58.6% |
| 4959972 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.57 | 44.0 | 3.79e-01 | 84.7% | 93.7% |
| 3928777 | 101.1.2.154 ↗ | alpha arrays › HTH › HTH › winged helix domain › CDT1_C | 0.57 | 41.0 | 3.39e-01 | 78.0% | 92.7% |
| 3900119 | 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 | 0.55 | 44.0 | 2.62e-01 | 91.5% | 81.3% |
| 3788392 | 101.1.2.535 ↗ | alpha arrays › HTH › HTH › winged helix domain › PF25889 | 0.55 | 42.0 | 3.52e-01 | 89.8% | 79.1% |
| 3466238 | 206.1.1.14 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1 | 0.53 | 40.0 | 2.42e-01 | 83.1% | 30.2% |
| 4945179 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.53 | 41.0 | 3.23e-01 | 89.8% | 72.4% |
| 3224878 | 101.1.15.1 ↗ | alpha arrays › HTH › HTH › HAT1, C-terminal domain › MOZ_SAS | 0.53 | 38.0 | 3.48e-01 | 83.1% | 87.8% |
| 4027178 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.53 | 42.0 | 3.65e-01 | 96.6% | 99.0% |
| 3712081 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.51 | 38.0 | 3.06e-01 | 79.7% | 83.6% |
| 4955611 | 101.1.2.48 ↗ | alpha arrays › HTH › HTH › winged helix domain › PadR | 0.50 | 38.0 | 3.31e-01 | 86.4% | 84.6% |
| 3594965 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.50 | 37.0 | 2.76e-01 | 78.0% | 48.6% |
| 4017372 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.50 | 37.0 | 2.92e-01 | 78.0% | 71.3% |