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DNA_ligase
Euk-VirBeAn_58058_virus
DNA_ligase__YP_009329769__BeAn_58058_virus__67082
Identity
- Accession:
- YP_009329769 ↗
- Protein ID:
- DNA_ligase
- Kingdom:
- euk
Quality
89.1
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Pokkesviricetes›
Chitovirales›
Poxviridae›
Oryzopoxvirus›
BeAn_58058_virus
TaxID: 67082
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 11-52
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01068.27 best | DNA_ligase_A_M | 35.4 | 1.30e-08 | 92.9% | 19.6% |
CATH (21)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3l2pA02 | 3.30.1490.70 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › | 0.89 | 74.0 | 6.20e-01 | 92.9% | 54.9% |
| 4d05A01 | 3.30.1490.70 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › | 0.84 | 69.0 | 5.74e-01 | 95.2% | 53.9% |
| 5d1oA02 | 3.30.1490.70 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › | 0.80 | 60.0 | 5.05e-01 | 95.2% | 47.9% |
| 2xgtA02 | 3.30.930.10 | Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 | 0.60 | 46.0 | 2.70e-01 | 83.3% | 26.4% |
| 3h8lA01 | 3.50.50.60 | Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain | 0.60 | 49.0 | 3.16e-01 | 95.2% | 27.3% |
| 2xssA00 | 3.30.450.40 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain | 0.58 | 47.0 | 3.35e-01 | 97.6% | 26.3% |
| 7xnzA02 | 3.10.580.10 | Alpha Beta › Roll › CBS-domain › CBS-domain | 0.58 | 48.0 | 3.51e-01 | 100.0% | 95.3% |
| 2a1xA00 | 2.60.120.620 | Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain | 0.57 | 44.0 | 2.91e-01 | 100.0% | 62.5% |
| 6p66D01 | 3.40.91.30 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › | 0.57 | 43.0 | 3.31e-01 | 88.1% | 68.8% |
| 5oyhD00 | 3.30.70.1230 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain | 0.56 | 47.0 | 3.13e-01 | 100.0% | 56.8% |
| 3ijmA00 | 3.90.1570.20 | Alpha Beta › Alpha-Beta Complex › tt1808, chain A › | 0.56 | 42.0 | 3.03e-01 | 100.0% | 26.0% |
| 1t6sA01 | 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 | 0.55 | 45.0 | 3.57e-01 | 100.0% | 44.2% |
| 6g9sA01 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.54 | 43.0 | 2.65e-01 | 97.6% | 53.6% |
| 3ec3A01 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.53 | 40.0 | 3.17e-01 | 97.6% | 70.5% |
| 4e4tA03 | 3.30.470.20 | Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain | 0.52 | 41.0 | 2.69e-01 | 88.1% | 34.2% |
| 1kw3B01 | 3.10.180.10 | Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 | 0.52 | 42.0 | 2.93e-01 | 92.9% | 28.0% |
| 1s7iA00 | 3.30.70.1060 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel | 0.51 | 42.0 | 3.03e-01 | 92.9% | 46.8% |
| 2z99A01 | 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 | 0.51 | 45.0 | 3.56e-01 | 100.0% | 71.3% |
| 6juvB01 | 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 | 0.51 | 43.0 | 3.63e-01 | 100.0% | 85.3% |
| 3rjlA02 | 3.40.309.10 | Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 | 0.50 | 41.0 | 2.69e-01 | 90.5% | 74.3% |
| 4pibA00 | 2.60.40.3910 | Mainly Beta › Sandwich › Immunoglobulin-like › Inclusion body protein | 0.50 | 39.0 | 2.68e-01 | 90.5% | 87.9% |
ECOD (24)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3795817 | 206.1.3.1 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_A_M | 0.92 | 83.0 | 4.95e-01 | 100.0% | 15.8% |
| 3633373 | 4095.1.1.2 ↗ | alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_M+DNA_ligase_A_N | 0.85 | 75.0 | 4.19e-01 | 100.0% | 9.9% |
| 3502952 | 4292.2.1.0 ↗ | a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain | 0.64 | 44.0 | 3.27e-01 | 85.7% | 30.0% |
| 4965617 | 2008.1.1.219 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF790 | 0.63 | 47.0 | 3.38e-01 | 83.3% | 59.2% |
| 4592824 | 323.1.1.0 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases | 0.62 | 50.0 | 3.44e-01 | 97.6% | 25.1% |
| 3980111 | 3281.1.1.2 ↗ | alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N | 0.58 | 45.0 | 2.56e-01 | 100.0% | 7.4% |
| 3455742 | 284.2.1.2 ↗ | a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain › DUF8223 | 0.58 | 46.0 | 4.21e-01 | 100.0% | 70.8% |
| 4975722 | 2003.1.5.24 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 | 0.58 | 45.0 | 2.88e-01 | 100.0% | 15.3% |
| 4029386 | 70.3.1.1 ↗ | beta barrels › beta-clip › SET domain-like › SET domain-like › SET | 0.58 | 45.0 | 2.90e-01 | 97.6% | 39.0% |
| 3297123 | 206.1.3.12 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL | 0.57 | 43.0 | 2.66e-01 | 83.3% | 67.7% |
| 3392468 | 101.21.1.1 ↗ | alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › TP6A_N | 0.57 | 48.0 | 3.64e-01 | 100.0% | 43.6% |
| 4003023 | 3110.1.1.2 ↗ | a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3-PglB_core | 0.56 | 45.0 | 3.36e-01 | 97.6% | 33.1% |
| 4673494 | 206.1.3.0 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp | 0.56 | 39.0 | 2.57e-01 | 95.2% | 13.5% |
| 3987298 | 5061.1.1.1 ↗ | alpha complex topology › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › SecY | 0.56 | 45.0 | 2.64e-01 | 92.9% | 58.1% |
| 5044026 | 242.2.1.2 ↗ | a+b two layers › Homing endonucleases-like › tRNA-intron endonuclease N-terminal domain-like › tRNA-intron endonuclease N-terminal domain-like › tRNA_int_endo_N | 0.55 | 35.0 | 2.86e-01 | 100.0% | 30.6% |
| 3749343 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.54 | 41.0 | 3.12e-01 | 83.3% | 55.0% |
| 3189438 | 2002.1.1.102 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PHP | 0.54 | 46.0 | 2.74e-01 | 100.0% | 13.8% |
| 4489860 | 2008.1.1.13 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RecU | 0.54 | 42.0 | 2.91e-01 | 100.0% | 23.0% |
| 4991375 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.53 | 40.0 | 3.17e-01 | 95.2% | 46.1% |
| 3365774 | 109.4.1.1560 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, E_motif | 0.53 | 45.0 | 2.66e-01 | 100.0% | 21.4% |
| 1197227 | 2485.1.1.0 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like | 0.53 | 40.0 | 3.17e-01 | 97.6% | 70.5% |
| 3724381 | 241.1.1.0 ↗ | a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone | 0.53 | 40.0 | 2.83e-01 | 83.3% | 70.3% |
| 3712052 | 109.4.1.745 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › OGFr_N | 0.52 | 46.0 | 2.84e-01 | 100.0% | 45.5% |
| 3634494 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.51 | 42.0 | 2.41e-01 | 95.2% | 8.0% |
D2
high
residues 60-203
Domain cluster:
rep: DNA_ligase_-2-__YP_010377156__Monkeypox_virus__10244__D413-557
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04679.22 best | DNA_ligase_A_C | 38.6 | 1.60e-09 | 75.7% | 94.7% |