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NC_070808.1__YP_010654219.1__PP504_gp52__00052

Bact-Vir

NC_070808.1__YP_010654219.1__PP504_gp52__00052

Identity

Accession:
NC_070808 ↗
Kingdom:
phage

Quality

83.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Beenievirus› Gordonia_phage_Dolores

TaxID: 2873534

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 27-75
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vyiA00 1.20.120.820 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Phosphoprotein, C-terminal domain 0.78 44.0 3.33e-01 79.6% 24.3%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 60.0 4.50e-01 89.8% 50.5%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.71 53.0 4.82e-01 81.6% 63.6%
7kfuC02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.69 52.0 3.33e-01 85.7% 17.2%
3nksA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.69 52.0 2.99e-01 81.6% 87.5%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 58.0 4.42e-01 91.8% 52.8%
2fnqA02 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.66 56.0 3.21e-01 91.8% 96.6%
1yx1A00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.65 32.0 2.02e-01 73.5% 8.8%
4e80C01 1.10.1410.10 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.64 50.0 3.25e-01 85.7% 74.9%
1kqfA02 3.40.50.740 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 47.0 3.00e-01 83.7% 20.9%
6ks6q01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.61 50.0 3.13e-01 91.8% 44.3%
4fhdA02 3.80.30.30 Alpha Beta › Alpha-Beta Horseshoe › pyruvate-formate lyase- activating enzyme › 0.60 44.0 2.83e-01 77.6% 16.7%
2wnsA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 41.0 2.66e-01 75.5% 25.4%
2uvaG11 6.10.60.10 Special › Helix non-globular › Hydrophobic Seed Protein › 0.57 32.0 3.18e-01 95.9% 43.6%
3p9dE01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.56 48.0 2.99e-01 95.9% 44.9%
1ultB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.56 42.0 2.40e-01 79.6% 9.4%
5ek8A01 2.60.40.3330 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 34.0 2.57e-01 73.5% 22.2%
1h2iA01 3.30.390.80 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › DNA repair protein Rad52/59/22 0.55 48.0 3.33e-01 93.9% 43.2%
5xuhA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.55 41.0 2.98e-01 79.6% 48.8%
6ks6Z01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.54 46.0 2.90e-01 95.9% 46.8%
5niiB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 46.0 3.01e-01 91.8% 76.5%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3730121 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.90 57.0 3.19e-01 98.0% 6.5%
3716174 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.89 59.0 4.38e-01 100.0% 30.9%
5026722 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.88 60.0 4.20e-01 100.0% 25.9%
4033043 616.1.1.41 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.85 53.0 4.25e-01 91.8% 34.4%
3592209 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.85 59.0 4.44e-01 100.0% 32.7%
4025655 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.78 59.0 4.60e-01 100.0% 41.1%
5039266 321.1.1.7 ↗ a+b two layers › Glutamine synthetase-like › Glutamine synthetase/guanido kinase › Glutamine synthetase/guanido kinase › GCS2 0.77 57.0 3.37e-01 79.6% 66.1%
3403813 603.2.1.12 ↗ alpha bundles › STAT-like › STAT › STAT › 7tm_7 0.77 62.0 3.65e-01 89.8% 11.6%
4982168 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.74 61.0 4.43e-01 89.8% 71.5%
5024938 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.73 60.0 4.37e-01 89.8% 70.8%
3931606 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.71 60.0 4.46e-01 91.8% 63.5%
3985490 192.2.1.5 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF4376 0.70 61.0 4.36e-01 91.8% 64.5%
4020403 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 0.70 55.0 3.17e-01 87.8% 9.7%
3790375 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.69 59.0 4.24e-01 91.8% 50.4%
4564040 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.68 61.0 4.25e-01 100.0% 34.1%
3783976 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.68 60.0 4.75e-01 100.0% 51.1%
4025072 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.67 60.0 4.36e-01 100.0% 40.0%
4972751 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.66 49.0 3.84e-01 81.6% 37.1%
3611219 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 55.0 3.22e-01 93.9% 21.2%
3229643 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.64 61.0 4.39e-01 100.0% 40.8%
4972761 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.64 48.0 3.01e-01 79.6% 59.2%
4890753 4342.1.1.2 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › YqgF 0.61 51.0 3.33e-01 91.8% 36.3%
3724474 207.1.1.85 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › F-box-like 0.61 48.0 2.82e-01 91.8% 9.2%
3647625 7581.1.1.39 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Chal_sti_synt_C, FAE1_CUT1_RppA 0.59 44.0 2.98e-01 81.6% 22.5%
3722860 2004.1.1.463 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin, Kinesin_assoc, Microtub_bd 0.58 51.0 2.95e-01 100.0% 10.2%
3970192 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 39.0 2.64e-01 91.8% 17.9%
3696633 3393.1.1.2 ↗ extended segments › CAA3-type cytochrome c oxidase subunit IV › CAA3-type cytochrome c oxidase subunit IV › CAA3-type cytochrome c oxidase subunit IV › Kinesin_assoc 0.57 50.0 4.00e-01 100.0% 49.5%
3520629 7523.1.1.20 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.57 38.0 2.79e-01 71.4% 82.9%
3683227 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.55 44.0 2.90e-01 87.8% 38.0%
4985007 7581.1.1.6 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Chal_sti_synt_C 0.51 37.0 2.86e-01 85.7% 51.0%
3608516 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.50 35.0 2.62e-01 75.5% 30.0%