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NC_024389.1__YP_009044952.1__HL57_gp40__00040

Bact-Vir

NC_024389.1__YP_009044952.1__HL57_gp40__00040

Identity

Accession:
NC_024389 ↗
Kingdom:
phage

Quality

89.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Unaquatrovirus› Leuconostoc_phage_phiLNTR2

TaxID: 1262523

Cluster

View cluster (78 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 16-91
PDB
Domain cluster: rep: MN095770.1__QFR57686.1__CPT_Slocum_129__00106__D10-79
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r60A01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.70 47.0 3.65e-01 93.4% 32.7%
1i94H01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.70 52.0 5.19e-01 92.1% 76.9%
3gkuA03 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.67 52.0 5.35e-01 94.7% 90.1%
3keyA02 3.30.1370.230 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Stn1, C-terminal wHTH domain 0.67 57.0 5.48e-01 93.4% 90.9%
2lrrA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.66 50.0 5.17e-01 100.0% 88.6%
2cxaA01 3.30.70.3550 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal domain 0.65 43.0 4.77e-01 92.1% 86.7%
3hz7A00 3.30.110.40 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › TusA-like domain 0.63 47.0 4.80e-01 92.1% 84.9%
7dg2C01 1.10.10.1200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › MAGE homology domain, winged helix WH1 motif 0.62 51.0 5.14e-01 94.7% 97.3%
4zcfC01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 51.0 3.60e-01 93.4% 33.9%
5xnsC00 1.10.10.580 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E 0.61 50.0 5.14e-01 96.1% 97.1%
6j0eB01 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 0.61 48.0 4.25e-01 100.0% 57.3%
3r0aA00 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 0.60 50.0 4.35e-01 100.0% 60.0%
1ub9A00 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 0.59 46.0 4.26e-01 100.0% 66.0%
3sb1A01 3.30.1370.140 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › HupH hydrogenase expression protein, C-terminal domain 0.59 49.0 4.54e-01 94.7% 89.9%
2p4wA01 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 0.58 46.0 4.23e-01 100.0% 65.0%
3ofgB00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.57 37.0 3.59e-01 94.7% 57.5%
1zkdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 46.0 3.59e-01 89.5% 52.9%
1jyoA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.57 40.0 3.33e-01 73.7% 46.2%
7pzaA02 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 0.56 47.0 4.58e-01 94.7% 82.6%
7n0eB02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.56 45.0 3.85e-01 88.2% 90.2%
1scjB00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.54 33.0 3.44e-01 78.9% 64.8%
1nf2A02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 44.0 4.00e-01 90.8% 85.8%
6upsA01 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.54 45.0 3.60e-01 93.4% 69.0%
1vbkA01 3.30.70.1510 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like 0.54 34.0 3.32e-01 96.1% 56.6%
2a8eA00 3.30.930.20 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Protein of unknown function DUF1054 0.54 40.0 2.97e-01 80.3% 59.5%
4gt8A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.53 45.0 3.78e-01 94.7% 96.2%
4pxdA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 39.0 3.38e-01 77.6% 91.3%
2ebbA00 3.30.1360.20 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Transcriptional coactivator/pterin dehydratase 0.53 36.0 3.43e-01 76.3% 57.3%
5i0dA05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 40.0 3.33e-01 93.4% 45.3%
3qfhA01 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.53 32.0 3.43e-01 80.3% 70.8%
3v97A03 3.30.750.80 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › RNA methyltransferase domain (HRMD) like 0.53 42.0 4.10e-01 89.5% 98.8%
2krhA00 1.10.10.1540 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Costar domain 0.53 43.0 4.17e-01 100.0% 82.4%
2weiA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 38.0 3.69e-01 80.3% 74.4%
6m36O01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.52 40.0 3.73e-01 82.9% 76.0%
4kr6A01 3.30.2130.30 Alpha Beta › 2-Layer Sandwich › VC0802-like › 0.51 41.0 3.25e-01 92.1% 40.9%
4ubtD00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.50 41.0 2.68e-01 92.1% 24.7%
2lnjA00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.50 36.0 2.89e-01 78.9% 90.6%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3517251 320.4.1.1 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › TIMELESS_C 0.71 64.0 5.85e-01 100.0% 79.0%
3902174 320.4.1.1 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › TIMELESS_C 0.71 64.0 5.73e-01 100.0% 72.4%
4247304 101.1.2.39 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA 0.69 53.0 5.66e-01 90.8% 96.9%
3218484 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.69 54.0 5.56e-01 96.1% 92.9%
4087039 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.68 59.0 5.82e-01 94.7% 90.0%
3515401 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 59.0 5.09e-01 96.1% 70.8%
3395627 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.67 53.0 5.36e-01 96.1% 88.0%
4031357 101.1.2.39 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA 0.67 53.0 5.54e-01 93.4% 92.9%
5036372 320.2.1.1 ↗ a+b two layers › R3H domain-like › Ribosomal protein S8, N-terminal domain › Ribosomal protein S8, N-terminal domain › Ribosomal_S8 0.67 51.0 5.45e-01 92.1% 93.8%
4028119 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.66 53.0 5.46e-01 93.4% 95.7%
3409254 101.1.2.393 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_MCM2 0.66 57.0 5.63e-01 94.7% 96.2%
3640641 320.4.1.1 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › TIMELESS_C 0.66 58.0 4.77e-01 100.0% 67.9%
5051083 328.7.1.1 ↗ a+b two layers › IF3-like › Smr domain › Smr domain › Smr 0.66 54.0 5.22e-01 92.1% 83.5%
4160174 320.4.1.1 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › TIMELESS_C 0.66 57.0 4.81e-01 100.0% 68.9%
5078802 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.65 53.0 5.49e-01 94.7% 97.1%
4347454 101.1.2.39 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA 0.65 53.0 5.47e-01 94.7% 98.6%
4228350 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.65 49.0 5.19e-01 93.4% 96.9%
3921829 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 49.0 5.26e-01 100.0% 96.9%
4640762 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 50.0 5.33e-01 90.8% 98.5%
5077595 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 51.0 4.59e-01 88.2% 61.8%
5016597 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.64 54.0 4.86e-01 94.7% 67.6%
4999182 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 50.0 5.09e-01 89.5% 88.0%
4951265 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 48.0 5.01e-01 90.8% 92.9%
3686379 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 51.0 5.28e-01 92.1% 98.6%
4361828 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.63 55.0 5.01e-01 100.0% 75.2%
3879109 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.63 55.0 5.00e-01 100.0% 76.0%
4008670 101.1.2.783 ↗ alpha arrays › HTH › HTH › winged helix domain › PF30336 0.62 50.0 5.15e-01 98.7% 98.6%
2037203 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.62 38.0 4.42e-01 77.6% 92.2%
4948041 328.9.1.0 ↗ a+b two layers › IF3-like › SepF C-terminal domain › SepF C-terminal domain 0.61 48.0 4.72e-01 92.1% 80.0%
3742570 101.1.2.65 ↗ alpha arrays › HTH › HTH › winged helix domain › Rad21_Rec8 0.61 50.0 4.66e-01 96.1% 71.0%
3167881 101.1.2.74 ↗ alpha arrays › HTH › HTH › winged helix domain › Cnd2 0.61 52.0 4.67e-01 98.7% 89.1%
3312445 101.21.1.1 ↗ alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › TP6A_N 0.60 54.0 4.53e-01 100.0% 76.9%
3827180 2484.1.1.110 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MULE 0.60 48.0 3.83e-01 90.8% 43.6%
3998806 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.60 49.0 5.07e-01 94.7% 97.1%
3530824 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.59 48.0 4.77e-01 96.1% 85.0%
3227306 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.59 46.0 4.69e-01 93.4% 86.7%
3202787 327.11.2.38 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_SLS1_1 0.59 38.0 3.93e-01 71.1% 70.0%
4999184 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 45.0 4.74e-01 100.0% 98.5%
3946945 101.1.2.274 ↗ alpha arrays › HTH › HTH › winged helix domain › SgrR_N 0.59 44.0 3.24e-01 100.0% 27.4%
5078002 2003.1.5.6 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltr_RsmB-F 0.59 50.0 3.39e-01 96.1% 31.1%
5048344 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 47.0 4.89e-01 89.5% 100.0%
4947165 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 46.0 3.63e-01 93.4% 39.4%
3800362 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.58 50.0 4.35e-01 100.0% 64.2%
3926227 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.58 42.0 2.81e-01 77.6% 47.9%
3390936 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.57 47.0 4.31e-01 90.8% 95.0%
3399905 7579.1.1.3 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S9 0.55 43.0 2.90e-01 86.8% 51.6%
3340064 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.54 48.0 4.28e-01 100.0% 71.8%
3908784 101.1.2.537 ↗ alpha arrays › HTH › HTH › winged helix domain › PF28339 0.54 44.0 4.51e-01 96.1% 98.6%
3971474 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 0.54 43.0 3.55e-01 88.2% 82.9%
3509710 3122.1.1.1 ↗ a+b complex topology › MESD › MESD › MESD › Mesd 0.52 38.0 3.23e-01 77.6% 48.8%
3273255 2003.1.5.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › FtsJ 0.52 40.0 3.09e-01 88.2% 34.0%
4873577 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.52 41.0 3.20e-01 86.8% 88.7%
3358446 2003.1.5.35 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › LCM 0.52 42.0 2.88e-01 93.4% 34.7%