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NC_008371.1__YP_764341.1__LPJV50_ORF27__00027

Bact-Vir

NC_008371.1__YP_764341.1__LPJV50_ORF27__00027

Identity

Accession:
NC_008371 ↗
Kingdom:
phage

Quality

62.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Skunavirus› Lactococcus_virus_jj50

TaxID: 213775

Cluster

View cluster (2 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 41-89
PDB
Domain cluster: rep: KP881232.1__AKE44836.1__Sm_phiM9_209__00205__D3-52
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24024.2 best DUF7336 55.1 6.90e-15 100.0% 78.3%
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.67 54.0 3.91e-01 93.9% 44.1%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.66 53.0 3.92e-01 91.8% 37.0%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.65 54.0 4.40e-01 98.0% 77.0%
6scxC01 3.90.79.20 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › 0.64 52.0 3.74e-01 100.0% 59.9%
6p3xB01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.63 50.0 3.49e-01 93.9% 50.3%
1z87A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 44.0 3.57e-01 79.6% 38.0%
1x9tA02 3.90.1620.10 Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 0.62 50.0 3.25e-01 98.0% 72.1%
2qlcA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.62 53.0 3.99e-01 100.0% 69.8%
4ud8A03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.61 47.0 3.38e-01 93.9% 46.2%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.61 52.0 4.10e-01 100.0% 49.1%
2hgsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.60 51.0 4.00e-01 100.0% 51.4%
1zldA00 2.60.40.1920 Mainly Beta › Sandwich › Immunoglobulin-like › Proteinaceous host-selective toxin ToxA 0.59 47.0 3.82e-01 91.8% 51.0%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.59 48.0 3.73e-01 95.9% 50.4%
1rlhA02 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.59 46.0 3.68e-01 87.8% 100.0%
5z9sA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 46.0 3.51e-01 89.8% 56.1%
2jovA01 3.10.530.10 Alpha Beta › Roll › CPE0013-like fold › CPE0013-like 0.58 41.0 3.79e-01 79.6% 56.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.58 45.0 3.83e-01 93.9% 57.6%
1b1zA02 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 42.0 3.20e-01 83.7% 75.0%
1cv8A00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 44.0 3.16e-01 93.9% 42.8%
3bgaA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 45.0 3.59e-01 93.9% 57.7%
4ll1C02 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 46.0 3.47e-01 100.0% 45.0%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.56 43.0 4.21e-01 100.0% 88.3%
2xzmZ00 3.30.1230.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › Ribosomal protein S21 0.56 39.0 3.29e-01 77.6% 51.5%
2atfA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 44.0 3.13e-01 100.0% 25.8%
5hccB02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.56 45.0 3.76e-01 95.9% 54.7%
6kryA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.56 41.0 3.09e-01 83.7% 75.4%
2hfqA00 3.10.510.10 Alpha Beta › Roll › NE1680-like fold › NE1680-like 0.55 44.0 3.88e-01 100.0% 71.8%
6x3aA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 44.0 3.66e-01 98.0% 60.6%
1qyaB01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.54 42.0 3.15e-01 89.8% 36.8%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.54 43.0 2.94e-01 100.0% 35.5%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.54 45.0 3.33e-01 100.0% 41.3%
3bzvB00 3.40.1690.10 Alpha Beta › 3-Layer(aba) Sandwich › name from scop › secretion proteins EscU 0.54 43.0 3.89e-01 100.0% 67.5%
1tljB00 3.30.1960.10 Alpha Beta › 2-Layer Sandwich › SSo0622-like fold › tRNA wybutosine-synthesizing-like 0.54 40.0 2.87e-01 89.8% 47.3%
1n26A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 41.0 3.68e-01 95.9% 57.7%
4dohB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 42.0 3.72e-01 100.0% 58.0%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.53 43.0 3.42e-01 100.0% 70.0%
1gsaA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.53 42.0 3.91e-01 93.9% 72.3%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.53 40.0 4.07e-01 87.8% 100.0%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 41.0 3.75e-01 100.0% 80.3%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 40.0 3.82e-01 95.9% 80.6%
2nytD00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.52 41.0 2.94e-01 95.9% 53.6%
2ebmA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.52 36.0 2.86e-01 79.6% 65.6%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.52 41.0 2.98e-01 100.0% 79.7%
3ke2B00 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 0.51 36.0 3.05e-01 79.6% 72.9%
4n5uA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.43e-01 100.0% 46.3%
1olzA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 40.0 2.42e-01 100.0% 16.4%
1tvgA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 39.0 2.99e-01 91.8% 39.0%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.50 36.0 2.74e-01 77.6% 73.2%
1o7fA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.50 37.0 2.86e-01 93.9% 31.6%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3721982 304.14.1.0 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.86 71.0 5.60e-01 89.8% 97.9%
5064795 264.2.1.1 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain › Topoisom_bac 0.85 72.0 5.32e-01 93.9% 98.3%
5042268 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.84 70.0 5.24e-01 91.8% 100.0%
3945393 7089.1.1.2 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › DUF5405 0.77 56.0 4.76e-01 77.6% 52.5%
3640039 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.77 63.0 4.45e-01 91.8% 37.3%
4032409 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.73 61.0 5.30e-01 93.9% 86.7%
5083843 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 55.0 4.51e-01 95.9% 54.7%
3582833 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.66 51.0 4.15e-01 93.9% 63.6%
3338688 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 51.0 4.73e-01 91.8% 93.8%
3413788 11.2.1.8 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PTEN_C2 0.65 55.0 4.05e-01 100.0% 40.0%
4973338 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.65 52.0 3.36e-01 100.0% 22.5%
3400537 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 54.0 4.35e-01 100.0% 57.7%
5031911 206.1.3.17 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DUF1297 0.64 54.0 3.42e-01 100.0% 20.4%
3614326 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.62 49.0 2.99e-01 93.9% 29.3%
5038450 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.62 53.0 3.34e-01 100.0% 86.3%
3274364 560.1.1.0 ↗ few secondary structure elements › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain 0.61 50.0 5.03e-01 95.9% 98.0%
3508957 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.61 51.0 3.78e-01 100.0% 45.5%
3170806 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.60 51.0 3.60e-01 100.0% 63.6%
1002433 11.10.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › Toxin_ToxA 0.59 47.0 3.82e-01 91.8% 50.5%
3194942 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 47.0 3.51e-01 98.0% 38.3%
5044314 3203.1.1.0 ↗ a+b two layers › Putative oxidoreductase › Putative oxidoreductase › Putative oxidoreductase 0.59 48.0 3.99e-01 91.8% 67.8%
3466470 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 46.0 3.54e-01 93.9% 69.2%
3766042 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.58 48.0 3.84e-01 100.0% 56.4%
4277768 223.2.1.52 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › GAP1-N2 0.56 39.0 2.92e-01 77.6% 31.0%
3323407 304.126.1.2 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C › V-ATPase_C 0.56 45.0 3.72e-01 100.0% 70.5%
3510040 3115.3.1.2 ↗ a+b two layers › GP2-like › P56 › P56 › DUF2922 0.56 42.0 3.81e-01 91.8% 78.8%
3712786 3346.1.1.0 ↗ a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.56 43.0 3.18e-01 100.0% 32.6%
3938229 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 46.0 3.46e-01 98.0% 51.5%
4153694 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.55 46.0 3.11e-01 95.9% 58.4%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.55 43.0 4.37e-01 93.9% 100.0%
3941732 3115.6.1.0 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon 0.55 43.0 4.29e-01 100.0% 98.0%
3312666 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 43.0 4.04e-01 100.0% 77.1%
2723970 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.54 45.0 3.52e-01 100.0% 57.9%
3181848 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 43.0 3.12e-01 100.0% 47.5%
5059379 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.54 42.0 3.92e-01 100.0% 100.0%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.53 39.0 3.84e-01 98.0% 98.3%
4987374 304.126.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.53 38.0 3.47e-01 85.7% 89.3%
3213645 267.1.1.0 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain 0.52 40.0 2.66e-01 93.9% 100.0%
3593291 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 38.0 2.76e-01 79.6% 28.3%
3576143 221.1.1.113 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_3 0.51 41.0 3.37e-01 100.0% 73.6%
4225807 272.1.1.0 ↗ a+b two layers › TolA/TonB C-terminal domain › TolA/TonB C-terminal domain › TolA/TonB C-terminal domain 0.51 36.0 3.30e-01 73.5% 56.9%
3491560 221.1.1.36 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N 0.51 39.0 3.38e-01 100.0% 51.1%