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DNA_topoisomerase_IIB
Euk-VirMicromonas_pusilla_virus_12T
DNA_topoisomerase_IIB__YP_007676289__Micromonas_pusilla_virus_12T__755272
Identity
- Accession:
- YP_007676289 ↗
- Protein ID:
- DNA_topoisomerase_IIB
- Kingdom:
- euk
Quality
89.4
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Algavirales›
Phycodnaviridae›
Prasinovirus›
Micromonas_pusilla_virus_12T
TaxID: 755272
Cluster
View cluster (39 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 47-235
Domain cluster:
rep: IMGVR_UViG_3300039190_000305-3300039190-Ga0399989_003201_3_1937__D82-97_167-336
D2
high
residues 241-378
Domain cluster:
rep: DNA_gyrase_subunit_B__YP_009352802__Kaumoebavirus_Viruses.__X__D311-415
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00204.32 best | DNA_gyraseB | 54.4 | 1.50e-14 | 97.8% | 55.2% |
D3
high
residues 387-534_569-661
Domain cluster:
rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D385-517_553-621_640-664
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01751.29 best | Toprim | 31.2 | 2.80e-07 | 49.0% | 84.4% |
| PF16898.11 | TOPRIM_C | 76.9 | 2.30e-21 | 39.4% | 67.2% |
CATH (23)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2zjtA01 | 3.40.50.670 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.84 | 42.0 | 6.08e-01 | 72.2% | 100.0% |
| 2xcqA01 | 3.40.50.670 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.73 | 56.0 | 6.32e-01 | 89.2% | 100.0% |
| 2c42A02 | 3.40.50.920 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.67 | 41.0 | 4.99e-01 | 85.5% | 92.4% |
| 3eeqA01 | 3.40.50.11220 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.64 | 32.0 | 4.47e-01 | 80.5% | 95.0% |
| 2qtfA01 | 3.40.50.11060 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › GTPase HflX, N-terminal domain | 0.64 | 28.0 | 4.22e-01 | 80.5% | 97.9% |
| 3gdwB00 | 3.40.50.510 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component | 0.62 | 34.0 | 4.31e-01 | 80.1% | 89.9% |
| 1pdoA00 | 3.40.50.510 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component | 0.62 | 33.0 | 4.39e-01 | 78.8% | 95.3% |
| 2qxyA00 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.61 | 31.0 | 4.34e-01 | 79.3% | 100.0% |
| 1r8jB01 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.60 | 33.0 | 4.13e-01 | 84.2% | 85.2% |
| 1qo0D01 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.60 | 31.0 | 4.21e-01 | 81.3% | 93.7% |
| 2vxbA02 | 3.40.50.10190 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › BRCT domain | 0.60 | 22.0 | 3.59e-01 | 82.6% | 93.8% |
| 3kznA01 | 3.40.50.1370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase | 0.59 | 32.0 | 3.89e-01 | 80.9% | 78.3% |
| 5mp7A02 | 3.40.50.2020 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.59 | 31.0 | 4.05e-01 | 78.8% | 89.7% |
| 3grfA01 | 3.40.50.1370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase | 0.58 | 27.0 | 3.48e-01 | 80.9% | 72.5% |
| 4f2gA01 | 3.40.50.1370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase | 0.58 | 29.0 | 3.56e-01 | 80.5% | 73.5% |
| 1js1Y01 | 3.40.50.1370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase | 0.58 | 32.0 | 3.82e-01 | 80.9% | 78.0% |
| 4r75A01 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.57 | 29.0 | 3.41e-01 | 91.3% | 67.5% |
| 6abiA01 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.56 | 33.0 | 4.24e-01 | 83.0% | 100.0% |
| 4qgsA01 | 3.40.50.1970 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.56 | 33.0 | 3.91e-01 | 83.4% | 81.7% |
| 3h8vB00 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.53 | 37.0 | 3.89e-01 | 83.8% | 76.1% |
| 2xtzB01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.53 | 36.0 | 3.92e-01 | 83.8% | 81.1% |
| 4am8E01 | 3.40.50.1370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase | 0.51 | 29.0 | 3.41e-01 | 80.9% | 76.6% |
| 4zdnA02 | 1.10.1240.100 | Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › | 0.51 | 22.0 | 3.32e-01 | 84.2% | 98.9% |
ECOD (31)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3551383 | 2006.1.3.3 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › Toprim,TOPRIM_C | 0.97 | 95.0 | 8.76e-01 | 100.0% | 99.7% |
| 3213306 | 2006.1.3.21 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › TOPRIM_C | 0.97 | 88.0 | 8.37e-01 | 92.5% | 100.0% |
| 3789608 | 2006.1.3.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain | 0.96 | 91.0 | 8.61e-01 | 96.7% | 98.5% |
| 3594652 | 2006.1.3.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain | 0.94 | 90.0 | 8.54e-01 | 97.5% | 99.3% |
| 1878568 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.88 | 49.0 | 6.73e-01 | 84.6% | 100.0% |
| 4878011 | 2006.1.3.21 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › TOPRIM_C | 0.88 | 69.0 | 7.38e-01 | 79.7% | 100.0% |
| 3964707 | 2006.1.3.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain | 0.88 | 71.0 | 7.27e-01 | 81.7% | 100.0% |
| 4238497 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.87 | 70.0 | 7.25e-01 | 82.2% | 100.0% |
| 3164150 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.87 | 67.0 | 7.02e-01 | 78.8% | 100.0% |
| 4124102 | 2006.1.3.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain | 0.86 | 72.0 | 7.23e-01 | 84.6% | 100.0% |
| 3520955 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.86 | 81.0 | 7.85e-01 | 97.1% | 97.7% |
| 2452014 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.83 | 69.0 | 7.01e-01 | 85.5% | 100.0% |
| None | — | 0.79 | 53.0 | 6.07e-01 | 90.0% | 88.0% | |
| 4945733 | 2006.1.3.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain | 0.77 | 72.0 | 7.13e-01 | 95.9% | 100.0% |
| None | — | 0.77 | 71.0 | 7.19e-01 | 94.6% | 100.0% | |
| None | — | 0.76 | 73.0 | 7.37e-01 | 98.8% | 99.6% | |
| 4406660 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.76 | 73.0 | 7.41e-01 | 100.0% | 100.0% |
| 5017203 | 7522.1.1.0 ↗ | a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like | 0.76 | 38.0 | 5.40e-01 | 71.0% | 100.0% |
| 4100838 | 2006.1.3.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim | 0.75 | 68.0 | 7.07e-01 | 93.8% | 100.0% |
| 5054900 | 7522.1.1.0 ↗ | a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like | 0.74 | 39.0 | 4.96e-01 | 85.1% | 82.7% |
| 4932292 | 7595.1.1.2 ↗ | a/b three-layered sandwiches › B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit › B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit › B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit › DUF6513 | 0.68 | 32.0 | 4.67e-01 | 80.5% | 97.3% |
| 4029893 | 7522.1.1.3 ↗ | a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like › OxoGdeHyase_C | 0.65 | 43.0 | 5.15e-01 | 86.3% | 98.1% |
| 3947905 | 2010.1.1.3 ↗ | a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man | 0.64 | 33.0 | 4.48e-01 | 79.7% | 94.4% |
| 3587277 | 2010.1.1.3 ↗ | a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man | 0.62 | 34.0 | 4.53e-01 | 82.2% | 97.7% |
| 3723137 | 7522.1.1.3 ↗ | a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like › OxoGdeHyase_C | 0.61 | 38.0 | 4.76e-01 | 90.0% | 99.3% |
| 3475517 | 2006.1.3.11 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › TOP6A-Spo11_Toprim | 0.61 | 43.0 | 4.45e-01 | 71.0% | 95.6% |
| 3817446 | 2006.1.3.21 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › TOPRIM_C | 0.61 | 44.0 | 5.11e-01 | 92.9% | 98.3% |
| 3175080 | 2003.1.1.0 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains | 0.60 | 36.0 | 4.54e-01 | 88.4% | 99.3% |
| 4935656 | 2003.1.1.123 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DUF166 | 0.55 | 30.0 | 3.70e-01 | 81.3% | 81.3% |
| 3278049 | 7579.1.1.0 ↗ | a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases | 0.54 | 35.0 | 4.00e-01 | 91.3% | 84.9% |
| 4270866 | 2007.12.1.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Beta-D-glucan exohydrolase, C-terminal domain › Beta-D-glucan exohydrolase, C-terminal domain | 0.53 | 37.0 | 4.23e-01 | 83.0% | 94.0% |
D4
high
residues 958-1070
Domain cluster:
rep: MH494197.1__AXC39168.1__X__00456__D116-252
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00521.27 best | DNA_topoisoIV | 35.4 | 8.20e-09 | 99.1% | 26.2% |
D5
medium
residues 668-779
Domain cluster:
rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D669-796
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00521.27 best | DNA_topoisoIV | 134.9 | 5.30e-39 | 100.0% | 25.5% |
D6
medium
residues 860-924
Domain cluster:
rep: IMGVR_UViG_3300007985_000017-3300007985-Ga0100381_100027569__D212-299