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SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00146

Bact-Vir

SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00146

Identity

Kingdom:
phage

Quality

77.4 mean pLDDT

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 36-132
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4lrjA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.69 47.0 5.32e-01 100.0% 94.5%
1ef0B02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.68 47.0 3.77e-01 87.6% 36.7%
3uc4A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.68 49.0 5.22e-01 100.0% 87.1%
6k3lB02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.67 50.0 5.14e-01 100.0% 82.4%
3rgfA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 48.0 4.87e-01 100.0% 76.0%
2c47A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 45.0 5.06e-01 100.0% 93.2%
4feuF01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 44.0 5.02e-01 99.0% 91.8%
2onlC01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 44.0 4.62e-01 100.0% 76.7%
1nxiA00 3.30.70.970 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RraB-like 0.65 47.0 4.28e-01 84.5% 56.1%
2clqA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.65 49.0 5.20e-01 100.0% 91.8%
6vp6A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.64 46.0 4.91e-01 100.0% 88.0%
1we8A01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.64 37.0 3.99e-01 90.7% 66.7%
4c8bA00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.64 48.0 3.41e-01 100.0% 27.6%
6blkC00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.63 55.0 4.72e-01 96.9% 76.6%
4qjvA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.62 37.0 3.87e-01 74.2% 62.9%
4l68A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 47.0 4.54e-01 100.0% 70.9%
1vkwA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.61 51.0 4.73e-01 92.8% 71.9%
3uimA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.61 45.0 4.68e-01 100.0% 84.3%
1g5hA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 51.0 3.68e-01 92.8% 75.8%
3netB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 49.0 3.50e-01 92.8% 89.3%
5xd6B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 44.0 4.51e-01 100.0% 81.9%
4gf3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.59 41.0 3.82e-01 100.0% 56.9%
1j5wB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 49.0 3.93e-01 92.8% 78.1%
2q7eA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 49.0 3.86e-01 92.8% 84.4%
6vh5C03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 43.0 4.46e-01 85.6% 84.3%
2joqA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 38.0 4.18e-01 75.3% 85.3%
1s9iB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 42.0 4.31e-01 100.0% 79.6%
4ozjA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 43.0 4.22e-01 86.6% 73.1%
3eeeA00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.58 48.0 3.89e-01 91.8% 47.3%
3m05B01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 46.0 4.73e-01 85.6% 90.2%
2kilA00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.57 46.0 3.80e-01 88.7% 50.3%
1ug8A00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.56 37.0 3.91e-01 79.4% 75.9%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 46.0 3.91e-01 91.8% 80.5%
1repC02 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 43.0 4.40e-01 83.5% 97.8%
2lrrA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.54 36.0 4.17e-01 86.6% 95.7%
8dy9I01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.54 47.0 3.77e-01 99.0% 91.7%
4bhqA00 3.30.70.2830 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 47.0 4.56e-01 97.9% 95.4%
1nbeB01 3.30.70.140 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Aspartate carbamoyltransferase regulatory subunit, N-terminal domain 0.53 43.0 4.37e-01 93.8% 91.4%
4jrnA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 47.0 4.19e-01 100.0% 93.6%
3kp0A03 3.30.30.60 Alpha Beta › 2-Layer Sandwich › Defensin A-like › D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain 0.50 28.0 3.25e-01 90.7% 77.6%
1g38A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 45.0 3.45e-01 100.0% 80.3%
2bolB02 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 44.0 3.98e-01 94.8% 97.7%
3evzA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 45.0 3.78e-01 100.0% 91.0%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3265038 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.69 50.0 3.51e-01 100.0% 24.3%
4279953 206.1.1.11 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.69 50.0 3.64e-01 100.0% 29.2%
4048671 206.1.1.76 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1, Pkinase_fungal 0.68 48.0 3.48e-01 100.0% 27.3%
3594100 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.67 48.0 3.39e-01 100.0% 24.3%
4934117 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.65 45.0 4.77e-01 82.5% 82.4%
4059572 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.65 46.0 4.42e-01 83.5% 64.5%
3671807 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.65 39.0 4.30e-01 93.8% 73.8%
5022418 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.64 38.0 4.43e-01 72.2% 86.2%
4080330 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.64 47.0 4.69e-01 83.5% 75.0%
3315396 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.63 44.0 3.04e-01 100.0% 21.9%
3602910 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.63 47.0 4.89e-01 90.7% 85.6%
5048329 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 0.63 56.0 4.89e-01 97.9% 77.9%
4064719 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.63 46.0 4.48e-01 82.5% 70.5%
4221596 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.63 46.0 4.42e-01 83.5% 66.1%
4128067 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.62 45.0 4.36e-01 83.5% 67.3%
4142447 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.62 46.0 4.61e-01 83.5% 76.0%
None — 0.62 47.0 2.89e-01 100.0% 13.2%
3949652 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.62 45.0 4.40e-01 82.5% 68.2%
4683313 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.62 46.0 4.35e-01 83.5% 65.0%
4574941 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.61 45.0 4.39e-01 83.5% 69.1%
3349852 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.61 47.0 3.33e-01 100.0% 26.7%
3385565 320.1.1.16 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › HP0268 0.61 41.0 4.47e-01 75.3% 84.6%
4205520 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.60 39.0 4.03e-01 74.2% 70.0%
3282598 225.1.1.0 ↗ 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 0.60 54.0 4.95e-01 99.0% 97.6%
3319796 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 43.0 2.93e-01 100.0% 20.9%
4115001 242.1.1.1 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.60 42.0 3.87e-01 84.5% 54.6%
4205746 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.60 46.0 4.47e-01 83.5% 75.2%
5045068 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 0.60 53.0 4.64e-01 100.0% 76.0%
4096306 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.59 45.0 4.27e-01 83.5% 67.8%
4086765 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.59 45.0 4.37e-01 83.5% 71.8%
3443064 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.59 40.0 3.81e-01 80.4% 58.3%
3382396 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 37.0 3.95e-01 74.2% 72.9%
3353024 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.58 43.0 3.07e-01 100.0% 26.4%
3165990 310.3.1.22 ↗ 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 › PF27480, PF30181 0.58 50.0 4.75e-01 95.9% 87.0%
4237486 242.1.1.1 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.58 40.0 3.44e-01 86.6% 44.5%
5000520 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 0.58 37.0 3.69e-01 74.2% 61.0%
4389430 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.57 43.0 4.19e-01 83.5% 70.9%
5030026 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.57 40.0 4.19e-01 85.6% 80.0%
4098100 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.57 47.0 3.52e-01 92.8% 85.7%
4681936 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.57 43.0 4.07e-01 83.5% 67.8%
137125 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.57 47.0 3.87e-01 91.8% 49.2%
2627446 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.56 47.0 3.81e-01 91.8% 46.8%
4983291 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.56 46.0 3.76e-01 92.8% 92.0%
2330628 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.56 46.0 3.76e-01 91.8% 47.6%
5010581 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 0.55 48.0 4.61e-01 100.0% 87.8%
7178 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.55 45.0 3.72e-01 91.8% 47.3%
5036575 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.55 44.0 3.60e-01 91.8% 89.3%
4114958 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.55 45.0 3.66e-01 92.8% 89.2%
4381821 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.55 45.0 3.60e-01 92.8% 90.5%
3623766 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 41.0 4.18e-01 82.5% 85.3%
3661475 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.53 40.0 3.43e-01 100.0% 49.1%
3177297 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.52 38.0 3.80e-01 83.5% 75.0%
3329478 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.52 41.0 3.85e-01 100.0% 70.0%
3248329 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.51 46.0 3.30e-01 100.0% 75.7%
3802419 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.51 45.0 3.43e-01 100.0% 71.5%
4116230 2003.1.5.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › FtsJ 0.51 46.0 3.73e-01 100.0% 90.6%
4188964 2003.1.5.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › FtsJ 0.51 46.0 3.64e-01 100.0% 83.5%
3358067 246.3.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos 0.50 44.0 3.17e-01 100.0% 80.3%