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NC_042025.1__YP_009613571.1__FDI52_gp42__00042

Bact-Vir

NC_042025.1__YP_009613571.1__FDI52_gp42__00042

Identity

Accession:
NC_042025 ↗
Kingdom:
phage

Quality

85.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nonagvirus› Salmonella_phage_SE1_(in:Nonagvirus)

TaxID: 2115848

Cluster

View cluster (10 members)

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 2-80
PDB
Domain cluster: rep: OP535472.1__UXR08034.1__X__00044__D122-210
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vugA05 3.30.70.3360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.80 44.0 5.48e-01 100.0% 89.6%
1xrsB01 3.30.30.60 Alpha Beta › 2-Layer Sandwich › Defensin A-like › D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain 0.73 44.0 5.26e-01 100.0% 92.3%
2y3uA02 3.30.980.50 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.72 53.0 4.63e-01 100.0% 54.0%
3luyA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.71 41.0 3.57e-01 100.0% 38.8%
2ewhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.70 39.0 3.79e-01 100.0% 49.4%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.70 38.0 3.79e-01 100.0% 50.6%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.69 49.0 4.97e-01 73.4% 80.8%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.69 48.0 5.08e-01 73.4% 81.7%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.69 52.0 4.74e-01 100.0% 61.0%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.67 45.0 4.35e-01 72.2% 61.4%
4bhqA00 3.30.70.2830 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 40.0 3.59e-01 100.0% 42.2%
2l2nA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.67 45.0 4.77e-01 70.9% 88.7%
5mmiU01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.66 39.0 3.88e-01 100.0% 54.9%
3mwbA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.65 38.0 3.60e-01 100.0% 47.9%
4nswA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 41.0 3.72e-01 98.7% 46.8%
2dn6A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 44.0 3.85e-01 100.0% 47.8%
1whnA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 47.0 4.34e-01 77.2% 60.4%
3pvlA04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 39.0 3.66e-01 96.2% 50.5%
4evuB00 3.30.1660.10 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › Flavin-binding protein dodecin 0.62 37.0 3.94e-01 100.0% 67.6%
5kolD00 3.90.950.20 Alpha Beta › Alpha-Beta Complex › Maf protein › CinA-like 0.62 42.0 3.34e-01 70.9% 79.1%
2x7gA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 36.0 3.55e-01 100.0% 52.3%
2elbA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 36.0 3.35e-01 97.5% 44.1%
3d3bJ00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 38.0 3.73e-01 100.0% 57.5%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.60 46.0 3.85e-01 84.8% 100.0%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 53.0 4.23e-01 100.0% 59.4%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 52.0 4.27e-01 98.7% 55.0%
2c47A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 37.0 3.82e-01 100.0% 67.1%
1x99A00 2.60.270.20 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › Cytolysin/lectin 0.58 40.0 3.31e-01 70.9% 54.5%
3uc4A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 35.0 3.50e-01 100.0% 57.6%
3iplB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.57 42.0 2.76e-01 79.7% 38.2%
4q9cA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 46.0 4.22e-01 89.9% 93.3%
1lc0A02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.56 39.0 3.27e-01 100.0% 40.1%
1vl4A01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.56 47.0 3.45e-01 91.1% 66.3%
7d27A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.56 38.0 2.79e-01 70.9% 27.4%
2wdtC02 3.30.1490.420 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Ubiquitin carboxyl-terminal hydrolase, domain 2 0.55 43.0 4.05e-01 86.1% 72.3%
1bakA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 3.30e-01 98.7% 46.2%
3oe3C00 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.54 44.0 4.26e-01 88.6% 85.2%
6v6aC01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 36.0 3.53e-01 98.7% 63.1%
1tltA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.54 38.0 2.92e-01 72.2% 33.3%
1i9zA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 48.0 3.17e-01 100.0% 26.5%
2hzmA02 2.20.140.20 Mainly Beta › Single Sheet › q64v53_bacfr protein fold › 0.54 44.0 4.30e-01 89.9% 81.2%
3vpbE00 2.20.28.160 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 33.0 3.65e-01 81.0% 87.5%
3plsA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 34.0 3.11e-01 100.0% 50.0%
2bkkA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 33.0 3.24e-01 100.0% 55.6%
5optY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 42.0 3.67e-01 89.9% 63.4%
1okjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 44.0 3.85e-01 98.7% 66.1%
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.51 44.0 3.89e-01 97.5% 70.5%
2pvaA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.51 43.0 2.92e-01 96.2% 88.5%
6htnA01 2.120.10.70 Mainly Beta › 6 Propeller › Neuraminidase › Fucose-specific lectin 0.51 34.0 2.86e-01 84.8% 39.4%
3rc2A02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.51 35.0 2.73e-01 70.9% 83.7%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4945414 304.12.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.86 55.0 5.27e-01 100.0% 57.8%
5074977 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 0.79 53.0 4.96e-01 100.0% 57.4%
5072591 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.78 52.0 4.57e-01 70.9% 47.0%
3426692 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.71 49.0 5.07e-01 72.2% 85.3%
3449957 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.70 50.0 4.67e-01 73.4% 65.3%
3299579 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.70 49.0 5.14e-01 72.2% 84.3%
3591080 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.70 39.0 3.96e-01 100.0% 53.8%
3234330 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.68 51.0 4.55e-01 78.5% 58.2%
3511524 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.67 40.0 3.50e-01 96.2% 40.0%
3209694 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.64 48.0 4.48e-01 79.7% 65.0%
3616729 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 47.0 4.32e-01 78.5% 60.6%
3585171 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.63 46.0 4.52e-01 75.9% 72.9%
3245175 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 46.0 4.33e-01 75.9% 65.3%
3918547 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 44.0 3.21e-01 100.0% 25.8%
5071707 304.19.1.4 ↗ a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › DUF2110_N 0.61 40.0 4.11e-01 100.0% 70.7%
5018724 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.61 54.0 5.15e-01 100.0% 91.6%
4011588 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.61 42.0 4.29e-01 70.9% 96.0%
3268152 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 0.61 43.0 2.81e-01 73.4% 28.5%
3914585 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.60 39.0 3.59e-01 96.2% 49.5%
3234134 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 2.79e-01 73.4% 30.3%
3878642 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.60 50.0 3.86e-01 93.7% 65.4%
3590547 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.59 48.0 4.16e-01 93.7% 90.8%
3517939 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 40.0 2.68e-01 73.4% 31.7%
3408369 284.1.3.4 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › CCTL2_WNK 0.56 42.0 4.37e-01 89.9% 86.7%
1100206 321.3.1.1 ↗ a+b two layers › Glutamine synthetase-like › C-terminal domain in VgrG › C-terminal domain in VgrG › ACD 0.55 45.0 2.95e-01 89.9% 48.3%
3308710 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 37.0 3.89e-01 70.9% 78.6%
3962129 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.55 35.0 3.03e-01 100.0% 40.0%
3473111 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.55 43.0 2.66e-01 86.1% 42.6%
1492426 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 37.0 3.08e-01 72.2% 61.7%
3601465 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.54 38.0 2.50e-01 73.4% 46.0%
3300147 206.1.1.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.54 38.0 2.54e-01 72.2% 68.9%
3248158 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 0.54 37.0 2.59e-01 73.4% 34.1%
3926768 206.1.1.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.54 43.0 2.86e-01 87.3% 72.9%
3582034 206.1.1.72 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Pkinase_fungal 0.53 42.0 2.84e-01 87.3% 69.2%
4000994 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 0.53 37.0 2.53e-01 72.2% 29.3%
4119979 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 36.0 2.46e-01 100.0% 18.4%
3270581 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 0.53 39.0 2.73e-01 82.3% 47.7%
3798803 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.52 36.0 2.50e-01 73.4% 58.0%
4644747 330.16.1.0 ↗ a+b two layers › dsRBD-like › ODA16 N-terminal domain › ODA16 N-terminal domain 0.52 39.0 3.96e-01 92.4% 81.2%
3502632 206.1.1.72 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Pkinase_fungal 0.52 36.0 2.48e-01 72.2% 30.8%
3240933 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 40.0 2.66e-01 84.8% 57.7%
3583235 206.1.1.72 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Pkinase_fungal 0.51 39.0 2.66e-01 84.8% 47.2%
3519115 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 38.0 2.60e-01 82.3% 44.6%
4986732 331.16.1.1 ↗ a+b two layers › TBP-like › TA0095-like › TA0095-like › DUF5611 0.51 35.0 3.65e-01 81.0% 82.9%
3517850 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.50 39.0 2.76e-01 87.3% 78.9%
3239526 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.50 37.0 2.86e-01 82.3% 70.0%