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integrase
Euk-VirHomarus_gammarus_nudivirus
integrase__YP_010087682__Homarus_gammarus_nudivirus__2509616
Identity
- Accession:
- YP_010087682 ↗
- Protein ID:
- integrase
- Kingdom:
- euk
Quality
76.9
mean pLDDT
Taxonomy
TaxID: 2509616
Cluster
View cluster (6 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 30-92
Domain cluster:
representative
CATH (22)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3s63A00 | 1.10.225.10 | Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like | 0.73 | 56.0 | 5.03e-01 | 82.5% | 62.5% |
| 3b9qA01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.69 | 52.0 | 4.64e-01 | 81.0% | 58.4% |
| 1sxjE03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.69 | 52.0 | 4.47e-01 | 81.0% | 95.9% |
| 1xriA00 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.67 | 56.0 | 4.27e-01 | 95.2% | 92.7% |
| 6fhpD00 | 1.10.390.10 | Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 | 0.64 | 51.0 | 5.17e-01 | 87.3% | 90.3% |
| 1t98A01 | 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 | 0.63 | 48.0 | 4.43e-01 | 85.7% | 78.2% |
| 2ph7A01 | 1.10.3400.10 | Mainly Alpha › Orthogonal Bundle › af_2093 domain like fold › af_2093 domain like | 0.62 | 53.0 | 4.36e-01 | 100.0% | 99.2% |
| 1sxjC03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.60 | 45.0 | 3.99e-01 | 81.0% | 95.8% |
| 3cjdA00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.60 | 51.0 | 3.75e-01 | 100.0% | 55.5% |
| 5xs2B02 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.59 | 51.0 | 4.10e-01 | 100.0% | 66.7% |
| 5nl6A02 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 43.0 | 3.64e-01 | 79.4% | 82.4% |
| 6jpaE00 | 1.20.140.150 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › | 0.57 | 43.0 | 3.34e-01 | 87.3% | 68.0% |
| 6eo5B01 | 3.30.465.10 | Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › | 0.57 | 49.0 | 3.34e-01 | 98.4% | 94.7% |
| 5z62E00 | 1.25.40.40 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI | 0.57 | 48.0 | 4.12e-01 | 100.0% | 66.1% |
| 1np7A02 | 1.25.40.80 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.56 | 47.0 | 3.98e-01 | 100.0% | 63.0% |
| 1tjcA00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.56 | 44.0 | 3.95e-01 | 90.5% | 71.6% |
| 3gw4A00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.55 | 44.0 | 3.26e-01 | 92.1% | 51.6% |
| 1o0sA02 | 1.20.1370.30 | Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › | 0.55 | 46.0 | 3.97e-01 | 100.0% | 63.9% |
| 1yxrA01 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.54 | 39.0 | 3.81e-01 | 81.0% | 86.5% |
| 3iqtA01 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.53 | 40.0 | 3.34e-01 | 81.0% | 64.9% |
| 1q6aA00 | 1.10.1240.30 | Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain | 0.52 | 44.0 | 3.83e-01 | 100.0% | 82.2% |
| 8ab6B02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.52 | 45.0 | 3.26e-01 | 100.0% | 74.6% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3214449 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.75 | 58.0 | 5.36e-01 | 82.5% | 68.8% |
| 1252580 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.74 | 57.0 | 5.03e-01 | 82.5% | 61.1% |
| 3285669 | 371.1.1.5 ↗ | few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › DUF1353 | 0.74 | 61.0 | 4.59e-01 | 92.1% | 43.2% |
| 4566333 | 186.1.1.1 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 | 0.72 | 61.0 | 5.26e-01 | 95.2% | 74.0% |
| 4177876 | 182.1.3.0 ↗ | alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX | 0.69 | 60.0 | 5.08e-01 | 96.8% | 70.5% |
| 5064030 | 182.1.3.0 ↗ | alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX | 0.69 | 60.0 | 5.31e-01 | 100.0% | 75.8% |
| 3758241 | 198.1.1.1 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2 | 0.68 | 50.0 | 4.49e-01 | 82.5% | 55.6% |
| 3505632 | 101.1.2.127 ↗ | alpha arrays › HTH › HTH › winged helix domain › Cullin_Nedd8 | 0.68 | 47.0 | 4.39e-01 | 81.0% | 57.5% |
| 3602903 | 101.1.3.0 ↗ | alpha arrays › HTH › HTH › tetra-helical, LuxR-like | 0.66 | 44.0 | 4.37e-01 | 74.6% | 66.2% |
| 3183788 | 192.29.1.149 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › ISN1 | 0.65 | 48.0 | 3.78e-01 | 79.4% | 76.3% |
| 4943072 | 101.1.8.0 ↗ | alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes | 0.63 | 54.0 | 4.60e-01 | 100.0% | 80.0% |
| 3728392 | 138.1.1.2 ↗ | 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 › Rep_fac_C | 0.63 | 45.0 | 4.00e-01 | 77.8% | 93.7% |
| 5040994 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.58 | 48.0 | 4.55e-01 | 90.5% | 84.0% |
| 3603105 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.57 | 45.0 | 4.26e-01 | 85.7% | 74.7% |
| 3427778 | 604.1.1.144 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF26575 | 0.56 | 46.0 | 4.32e-01 | 92.1% | 93.8% |
| 5081092 | 601.7.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN | 0.55 | 39.0 | 3.27e-01 | 77.8% | 65.9% |
| 3660897 | 2004.1.1.0 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases | 0.52 | 44.0 | 3.16e-01 | 100.0% | 32.7% |
| 3899959 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.51 | 38.0 | 3.35e-01 | 85.7% | 88.6% |
| 3289465 | 2008.1.1.123 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF6119 | 0.51 | 42.0 | 3.05e-01 | 93.7% | 68.8% |
D2
medium
residues 107-276
Domain cluster:
rep: MK448963.1__QBX29522.1__Javan498_0048__00001__D46-231
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00589.28 best | Phage_integrase | 56.9 | 3.30e-15 | 99.4% | 85.5% |