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LSDeep1_scaffold_41_prodigal-single.1__X__X__00048

Bact-Vir

LSDeep1_scaffold_41_prodigal-single.1__X__X__00048

Identity

Kingdom:
phage

Quality

87.9 mean pLDDT

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 3-129
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.81 75.0 7.49e-01 98.4% 99.2%
2l25A00 3.30.2000.20 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.80 76.0 7.31e-01 100.0% 96.5%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.79 74.0 7.22e-01 100.0% 97.1%
4acvA00 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.78 67.0 6.93e-01 100.0% 96.6%
4hudA01 3.30.2000.40 Alpha Beta › 2-Layer Sandwich › STM4215-like › Myoviridae tail sheath stabiliser 0.76 71.0 5.92e-01 100.0% 80.5%
3fz2A00 3.30.70.1700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phage minor tail protein U 0.73 67.0 6.71e-01 99.2% 99.2%
1bdfA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.70 45.0 4.87e-01 85.8% 76.4%
2vqeE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 28.0 3.75e-01 73.2% 71.9%
3eeeA00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.67 48.0 4.21e-01 95.3% 50.0%
1v8cA02 3.30.1370.80 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain 0.67 38.0 4.65e-01 72.4% 87.5%
2y3uA02 3.30.980.50 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.67 51.0 5.35e-01 100.0% 89.4%
3d85D02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 40.0 4.36e-01 85.8% 72.6%
8c46A01 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 43.0 4.57e-01 84.3% 76.3%
3pcoB06 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.64 40.0 4.53e-01 96.1% 84.0%
2vzsA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 38.0 4.10e-01 75.6% 68.2%
2x8kA01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.63 46.0 5.02e-01 96.9% 91.4%
2e7vA01 3.30.70.960 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › SEA domain 0.62 37.0 3.99e-01 100.0% 69.5%
4o38A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 40.0 4.47e-01 81.9% 85.4%
5uejA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 42.0 4.45e-01 88.2% 77.2%
2f7vA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 42.0 4.50e-01 91.3% 81.5%
1jz7A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 39.0 4.08e-01 86.6% 70.4%
1wleA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 55.0 4.11e-01 99.2% 78.2%
2q7eA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 53.0 4.48e-01 98.4% 94.3%
4illB01 2.40.30.310 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 44.0 4.56e-01 85.0% 84.5%
3mdyA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 35.0 3.78e-01 79.5% 67.3%
3a7fA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 35.0 3.91e-01 95.3% 77.4%
3netB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 53.0 3.98e-01 100.0% 94.0%
3uiuA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 36.0 4.06e-01 80.3% 80.4%
4jdzA02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 44.0 4.04e-01 78.7% 81.8%
3eniC00 2.50.10.10 Mainly Beta › Clam › Bacteriochlorophyll-a Protein › Bacteriochlorophyll A 0.58 48.0 3.56e-01 90.6% 46.6%
3rd6A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.58 42.0 4.07e-01 75.6% 88.2%
3icaB00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.58 53.0 4.45e-01 98.4% 99.5%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.58 53.0 4.10e-01 100.0% 94.2%
3kojB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 26.0 2.97e-01 95.3% 53.3%
6nhiA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 51.0 3.77e-01 98.4% 97.9%
1qe0A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 52.0 3.95e-01 100.0% 92.9%
4qnyA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.56 36.0 3.72e-01 78.7% 68.9%
3rqwA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.56 49.0 4.34e-01 97.6% 93.2%
1yc9A02 2.20.200.10 Mainly Beta › Single Sheet › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.55 29.0 3.47e-01 90.6% 74.7%
3nrfA00 2.60.40.4110 Mainly Beta › Sandwich › Immunoglobulin-like › Protein of unknown function DUF4354 0.55 37.0 4.09e-01 85.8% 85.3%
3byqA00 3.30.1330.110 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › BB2672 0.55 44.0 3.82e-01 84.3% 88.5%
4g2aA01 2.60.40.3680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 49.0 3.96e-01 98.4% 60.7%
3lvtA03 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 37.0 3.78e-01 90.6% 71.3%
1cwvA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 40.0 4.41e-01 87.4% 98.0%
4wsqB00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.53 41.0 3.05e-01 81.9% 43.2%
3a27A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 37.0 3.12e-01 80.3% 43.8%
3qfgA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 41.0 4.00e-01 88.2% 77.9%
4c57B00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.51 39.0 2.96e-01 81.9% 46.1%
3w1eA01 3.30.1660.40 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › FlgT, N-terminal domain 0.50 32.0 3.72e-01 78.7% 91.1%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.50 42.0 4.12e-01 89.0% 88.8%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2642577 304.124.1.3 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.81 76.0 7.45e-01 99.2% 97.0%
3964886 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.81 74.0 7.12e-01 96.9% 98.6%
5454 304.124.1.2 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Gp37 0.80 74.0 7.25e-01 99.2% 97.8%
3966645 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.79 72.0 7.27e-01 96.9% 98.4%
4034134 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.79 71.0 7.23e-01 96.9% 100.0%
4883824 304.124.1.6 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF5072 0.78 70.0 6.97e-01 100.0% 93.0%
4928893 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.78 72.0 6.85e-01 100.0% 97.9%
5040945 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.77 72.0 6.75e-01 100.0% 96.7%
3970985 304.124.1.9 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.76 70.0 6.77e-01 100.0% 100.0%
4034595 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.75 67.0 6.87e-01 97.6% 100.0%
5083880 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.75 69.0 6.61e-01 100.0% 99.3%
3776086 306.10.1.5 a+b two layers › Glucose permease domain IIB-like › H1 domain of KCTD12 › H1 domain of KCTD12 › PF31088 0.74 41.0 4.09e-01 76.4% 52.3%
4562028 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.72 57.0 5.48e-01 100.0% 73.1%
4988097 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.72 67.0 6.69e-01 98.4% 99.2%
3802659 304.8.1.66 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF7049 0.71 48.0 5.24e-01 81.1% 82.9%
4057397 305.1.1.1 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.70 46.0 4.82e-01 84.3% 73.0%
4196274 305.1.1.1 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.70 46.0 4.82e-01 77.2% 73.0%
3949263 304.124.1.9 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.70 55.0 6.04e-01 86.6% 100.0%
4342449 305.1.1.1 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.69 46.0 4.73e-01 77.2% 70.8%
4169524 305.1.1.1 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.69 45.0 4.74e-01 85.8% 73.0%
3554056 11.1.1.134 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL12p40_C 0.69 47.0 4.76e-01 89.8% 70.4%
2553760 304.12.1.1 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › Ribosomal_S6 0.66 47.0 5.05e-01 92.1% 86.8%
3857701 314.1.1.0 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.66 60.0 4.47e-01 100.0% 85.9%
4069303 304.153.1.1 a+b two layers › Alpha-beta plaits › Collagenase G catalytic helper subdomain › Collagenase G catalytic helper subdomain › ColG_sub 0.66 50.0 5.20e-01 99.2% 85.8%
4028502 305.1.1.0 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.66 44.0 4.58e-01 76.4% 72.5%
3915879 304.12.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.65 44.0 4.67e-01 85.0% 79.1%
4136515 310.3.1.23 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › RP854 0.64 58.0 5.37e-01 97.6% 78.1%
3449841 310.3.1.14 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › DUF7049 0.63 45.0 5.19e-01 75.6% 100.0%
3336425 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 43.0 4.29e-01 86.6% 66.7%
3344799 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 43.0 4.21e-01 76.4% 63.6%
4264016 304.44.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.62 40.0 4.46e-01 92.1% 85.3%
3224729 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 44.0 4.95e-01 90.6% 100.0%
3507153 2484.1.1.39 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Fumble 0.61 38.0 2.74e-01 84.3% 22.9%
3750856 314.1.1.0 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.60 54.0 4.02e-01 97.6% 76.2%
3902949 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 42.0 3.36e-01 97.6% 36.7%
3962890 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.59 36.0 3.72e-01 99.2% 62.4%
3929879 11.12.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.59 45.0 4.15e-01 88.2% 62.2%
3699188 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.59 38.0 2.88e-01 79.5% 25.6%
5018915 225.1.1.3 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.59 51.0 4.74e-01 100.0% 74.4%
4937367 504.1.1.0 a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB 0.59 35.0 3.53e-01 98.4% 60.0%
5072584 2003.1.5.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.58 42.0 3.24e-01 98.4% 32.7%
5066585 881.2.1.0 a+b three layers › Mog1p/PsbP-like › TM1622-like › TM1622-like 0.57 42.0 4.17e-01 95.3% 74.6%
3356898 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.56 34.0 3.26e-01 89.0% 50.7%
3434668 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 40.0 3.82e-01 85.8% 63.3%
3944238 2485.3.1.7 a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside 0.55 45.0 3.51e-01 89.0% 95.1%
3643481 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 43.0 3.06e-01 82.7% 40.5%
3213160 11.12.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.55 49.0 4.38e-01 100.0% 84.9%
3510174 11.12.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.54 48.0 4.11e-01 99.2% 83.3%
3476907 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 41.0 3.06e-01 81.1% 44.4%
3941539 1.1.13.40 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_min_tail 0.53 41.0 4.38e-01 86.6% 99.0%
3901366 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 41.0 3.00e-01 81.9% 40.6%
4012647 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.52 40.0 2.92e-01 82.7% 46.8%
3495018 11.12.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.52 46.0 3.89e-01 100.0% 75.9%
5037015 504.1.1.0 a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB 0.51 32.0 3.17e-01 99.2% 57.8%
3230573 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 39.0 2.86e-01 81.9% 37.6%
3694611 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 39.0 2.84e-01 81.9% 40.9%
3922900 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 39.0 2.91e-01 81.9% 41.9%
3678424 206.1.1.70 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.51 40.0 2.91e-01 82.7% 40.0%
3194447 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 39.0 2.85e-01 81.9% 43.0%