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ATP-dependent_DNA_ligase
Euk-VirOnly_Syngen_Nebraska_virus_5
ATP-dependent_DNA_ligase__YP_009325800__Only_Syngen_Nebraska_virus_5__1917232
Identity
- Accession:
- YP_009325800 ↗
- Protein ID:
- ATP-dependent_DNA_ligase
- Kingdom:
- euk
Quality
87.3
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Algavirales›
Phycodnaviridae›
Chlorovirus›
Only_Syngen_Nebraska_virus_5
TaxID: 1917232
Cluster
View cluster (52 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 191-292
Domain cluster:
rep: MK256384.1__QBA85097.1__X__00002__D37-130
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF14743.13 best | DNA_ligase_OB_2 | 66.9 | 1.80e-18 | 66.7% | 89.4% |
D2
medium
residues 1-27_138-188
D3
medium
residues 28-137
Domain cluster:
rep: ATP-dependent_DNA_ligase__YP_009094561__Melbournevirus__1560514__D164-283
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1fviA03 | 3.30.470.30 | Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme | 0.98 | 90.0 | 9.34e-01 | 97.3% | 100.0% |
| 6imjA01 | 3.30.470.30 | Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme | 0.82 | 77.0 | 6.31e-01 | 100.0% | 61.7% |
| 1a0iA03 | 3.30.470.30 | Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme | 0.76 | 69.0 | 6.22e-01 | 98.2% | 100.0% |
| 1ckmA01 | 3.30.470.30 | Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme | 0.66 | 60.0 | 5.25e-01 | 99.1% | 67.7% |
| 1wteA02 | 3.40.1560.10 | Alpha Beta › 3-Layer(aba) Sandwich › type ii restriction endonuclease, domain 2 › type ii restriction endonuclease, domain 2 | 0.62 | 40.0 | 3.93e-01 | 97.3% | 58.9% |
| 1g29103 | 2.40.50.100 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain | 0.60 | 36.0 | 4.35e-01 | 98.2% | 100.0% |
| 4i1tA02 | 3.30.70.2640 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Arenavirus RNA polymerase | 0.58 | 40.0 | 4.52e-01 | 96.4% | 94.0% |
| 3w5xA00 | 3.30.70.1350 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cation efflux protein, cytoplasmic domain | 0.57 | 37.0 | 4.17e-01 | 80.9% | 91.3% |
| 2ql8A00 | 3.30.300.20 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain | 0.57 | 44.0 | 4.07e-01 | 81.8% | 65.7% |
| 6he0A01 | 3.30.300.30 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain | 0.55 | 36.0 | 3.65e-01 | 79.1% | 67.3% |
| 2ygwA02 | 3.40.630.150 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Malonyl-CoA decarboxylase, catalytic domain | 0.54 | 44.0 | 3.47e-01 | 93.6% | 72.2% |
| 4oycB00 | 3.30.300.30 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain | 0.52 | 35.0 | 3.86e-01 | 81.8% | 86.5% |
| 3gkuC02 | 3.30.300.20 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain | 0.52 | 36.0 | 3.98e-01 | 81.8% | 91.0% |
ECOD (22)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1245394 | 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 | 0.97 | 94.0 | 7.55e-01 | 100.0% | 58.2% |
| 3387834 | 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 | 0.78 | 73.0 | 6.00e-01 | 100.0% | 59.5% |
| 5058450 | 316.1.1.27 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta | 0.60 | 42.0 | 4.08e-01 | 80.9% | 64.0% |
| 5028076 | 316.1.1.2 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 | 0.56 | 41.0 | 3.75e-01 | 81.8% | 57.2% |
| 5016879 | 316.1.1.27 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta | 0.56 | 42.0 | 4.09e-01 | 81.8% | 72.5% |
| 4465859 | 316.1.1.30 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PAP_NTPase | 0.55 | 41.0 | 3.59e-01 | 80.0% | 65.9% |
| 5882 | 324.1.1.1 ↗ | a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC | 0.54 | 42.0 | 3.87e-01 | 82.7% | 68.8% |
| 4629797 | 327.11.1.2 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KhpA-B_KH | 0.54 | 35.0 | 4.09e-01 | 93.6% | 96.0% |
| 3176440 | 327.7.1.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like | 0.54 | 42.0 | 4.36e-01 | 99.1% | 89.5% |
| 5043433 | 316.1.1.2 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 | 0.53 | 38.0 | 3.83e-01 | 80.9% | 73.0% |
| 3171583 | 327.7.1.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like | 0.53 | 42.0 | 4.32e-01 | 99.1% | 89.5% |
| 4138757 | 324.1.1.1 ↗ | a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC | 0.52 | 40.0 | 3.73e-01 | 81.8% | 70.7% |
| 3330375 | 224.1.1.2 ↗ | a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin | 0.52 | 31.0 | 3.46e-01 | 93.6% | 75.3% |
| 4600279 | 316.1.1.9 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › GlnE | 0.52 | 44.0 | 3.20e-01 | 91.8% | 53.8% |
| 4223149 | 327.4.1.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › YhbC-like, N-terminal domain › YhbC-like, N-terminal domain › RimP_N | 0.52 | 36.0 | 3.94e-01 | 79.1% | 92.9% |
| 3730197 | 327.7.1.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer | 0.52 | 34.0 | 3.72e-01 | 80.0% | 82.2% |
| 3271214 | 327.5.1.2 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C | 0.52 | 37.0 | 3.54e-01 | 81.8% | 62.2% |
| 3472529 | 109.6.1.3 ↗ | alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF_N | 0.52 | 34.0 | 2.93e-01 | 98.2% | 43.5% |
| 1019401 | 327.11.1.2 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KhpA-B_KH | 0.52 | 36.0 | 3.98e-01 | 81.8% | 91.0% |
| 4014817 | 327.7.1.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like | 0.51 | 35.0 | 3.88e-01 | 99.1% | 92.9% |
| 4982246 | 3521.1.1.0 ↗ | a+b three layers › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain | 0.50 | 37.0 | 3.83e-01 | 93.6% | 85.0% |
| 4980949 | 327.5.1.2 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C | 0.50 | 34.0 | 3.77e-01 | 78.2% | 90.6% |