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NC_024392.1__YP_009045062.1__LP114_007__00007

Bact-Vir

NC_024392.1__YP_009045062.1__LP114_007__00007

Identity

Accession:
NC_024392 ↗
Kingdom:
phage

Quality

84.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Homburgvirus› Listeria_phage_LP-114

TaxID: 1458857

Cluster

View cluster (15 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 medium residues 22-42_107-183
PDB
Domain cluster: rep: OP172801.1__WAX15524.1__EG103P1_00060__00060__D24-50_115-221
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1tpmA00 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.74 32.0 4.40e-01 80.6% 80.0%
2ci8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.71 32.0 4.17e-01 78.6% 75.0%
1khiA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 44.0 5.00e-01 72.4% 100.0%
1wibA00 3.30.1550.10 Alpha Beta › 2-Layer Sandwich › Ribosomal protein L11, N-terminal domain › Ribosomal protein L11/L12, N-terminal domain 0.62 45.0 4.65e-01 78.6% 80.4%
6l4qB01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 44.0 3.99e-01 77.6% 74.1%
1rpyB00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.58 33.0 3.50e-01 83.7% 64.0%
4trtA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.57 39.0 3.62e-01 70.4% 83.6%
2kknA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.57 39.0 3.38e-01 71.4% 100.0%
1g29102 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 23.0 3.14e-01 75.5% 73.3%
1vpkA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.56 39.0 3.67e-01 72.4% 85.8%
6ap4B02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.56 39.0 3.49e-01 72.4% 76.6%
3ifvC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.56 40.0 3.06e-01 75.5% 44.6%
5fxdA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.55 42.0 3.21e-01 80.6% 85.0%
2hy1A00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.55 38.0 2.96e-01 71.4% 99.6%
3zleA03 2.10.70.70 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.53 23.0 3.22e-01 75.5% 94.9%
5i47B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 42.0 4.33e-01 94.9% 92.6%
4up7A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 47.0 4.06e-01 99.0% 71.1%
1sxjH02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 38.0 3.50e-01 76.5% 87.5%
2pn1A03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.52 43.0 4.07e-01 92.9% 95.0%
2y8tA03 2.10.70.70 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.51 26.0 3.21e-01 85.7% 81.8%
1u7bA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.50 43.0 3.21e-01 93.9% 94.4%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4334411 896.1.1.1 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Ribosomal_L38e 0.75 29.0 3.54e-01 76.5% 53.8%
3347257 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 49.0 4.66e-01 85.7% 90.4%
4026577 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.58 27.0 3.48e-01 80.6% 76.4%
4027686 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.58 26.0 3.36e-01 80.6% 72.7%
4024768 330.3.1.7 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like › AP2 0.58 26.0 3.39e-01 81.6% 74.5%
4964125 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.57 44.0 3.30e-01 83.7% 96.2%
5991 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.57 41.0 3.85e-01 75.5% 86.1%
5050610 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 39.0 4.38e-01 70.4% 100.0%
3535276 2.6.1.0 ↗ beta barrels › OB-fold › Staphylococcal nuclease › Staphylococcal nuclease 0.56 41.0 4.01e-01 77.6% 78.2%
1290662 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.55 39.0 3.55e-01 76.5% 79.7%
3479948 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.54 39.0 2.88e-01 76.5% 71.9%
3238522 2008.1.1.27 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAI1 0.54 47.0 3.35e-01 99.0% 71.4%
4987233 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.54 30.0 3.23e-01 74.5% 62.4%
3638151 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.52 45.0 3.92e-01 96.9% 74.7%
4029445 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.51 25.0 3.11e-01 76.5% 78.2%
D2 medium residues 43-106_184-216
PDB
Domain cluster: rep: IMGVR_UViG_3300025326_000018-3300025326-Ga0209342_1000012799__D71-126_218-239
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cfoA04 1.10.8.70 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 0.64 28.0 3.64e-01 77.3% 72.2%
7t7kA01 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.63 48.0 4.52e-01 81.4% 95.8%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.58 40.0 3.98e-01 71.1% 99.0%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.58 35.0 4.08e-01 78.4% 89.4%
3fdfA02 6.10.140.550 Special › Helix non-globular › Helix Hairpins › 0.56 28.0 3.46e-01 96.9% 78.6%
3cexA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.55 40.0 3.41e-01 76.3% 91.8%
2ahfA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.55 42.0 2.82e-01 81.4% 90.5%
3nkhA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.54 43.0 3.24e-01 83.5% 69.2%
5l3wA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.54 33.0 3.47e-01 76.3% 66.7%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4485576 1.1.17.4 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Peptidase_S64 0.65 47.0 3.28e-01 74.2% 65.5%
2755028 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.62 44.0 4.15e-01 77.3% 61.7%
3517579 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.62 44.0 4.76e-01 80.4% 88.7%
3469354 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.61 43.0 4.06e-01 78.4% 61.7%
4011601 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.58 43.0 3.79e-01 77.3% 66.4%
3668571 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.58 42.0 3.28e-01 77.3% 70.5%
5048239 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.51 44.0 4.24e-01 96.9% 96.5%
3905558 150.3.1.17 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › SCF 0.51 41.0 3.55e-01 83.5% 81.4%
3218916 614.1.1.1 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › L27 0.50 31.0 3.72e-01 71.1% 98.3%