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NC_009813.1__YP_001468762.1__LiPB054_gp58__00058

Bact-Vir

NC_009813.1__YP_001468762.1__LiPB054_gp58__00058

Identity

Accession:
NC_009813 ↗
Kingdom:
phage

Quality

81.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_B054

TaxID: 330397

Cluster

Singleton — not in a non-trivial cluster

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 53-102
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7ob9B02 3.90.1800.10 Alpha Beta › Alpha-Beta Complex › DCoH-like › RNA polymerase alpha subunit dimerisation domain 0.54 44.0 3.49e-01 100.0% 45.1%
3e07A00 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.53 32.0 2.72e-01 86.0% 31.1%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.53 39.0 3.08e-01 84.0% 86.7%
7onnA01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.52 37.0 3.46e-01 80.0% 95.6%
2hlyA00 3.10.550.10 Alpha Beta › Roll › Atu2299-like › Hypothetical protein Atu2299 0.51 37.0 2.59e-01 84.0% 65.4%
5a48B00 3.30.420.610 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › LOTUS domain-like 0.51 37.0 3.12e-01 80.0% 88.5%
1q57G01 2.20.25.180 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.51 33.0 3.06e-01 72.0% 46.6%
4umgA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.03e-01 82.0% 85.3%
1v9kA00 3.30.2350.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › Pseudouridine synthase 0.51 36.0 2.49e-01 82.0% 54.6%
4okeA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 37.0 2.73e-01 86.0% 83.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4034336 4.8.1.13 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › ComK 0.57 39.0 2.91e-01 74.0% 80.7%
4032923 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.56 40.0 2.46e-01 80.0% 36.8%
4985007 7581.1.1.6 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Chal_sti_synt_C 0.55 39.0 2.95e-01 80.0% 88.8%
3371393 4266.2.1.1 ↗ alpha bundles › Hyaluronidase domain-like › TTHA0068-like › TTHA0068-like › DUF309 0.53 36.0 2.54e-01 72.0% 75.3%
1807451 3702.1.1.2 ↗ beta complex topology › Penicillin binding protein dimerisation domain › Penicillin binding protein dimerisation domain › Penicillin binding protein dimerisation domain › PBP_dimer_2 0.52 40.0 3.37e-01 84.0% 89.7%
3727030 11.1.5.20 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › NDT80_PhoG 0.52 43.0 2.96e-01 100.0% 40.0%
3472375 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 39.0 3.28e-01 86.0% 71.1%
3483568 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 40.0 2.34e-01 86.0% 35.7%
5054141 2.14.1.0 ↗ beta barrels › OB-fold › HupF/HypC-like › HupF/HypC-like 0.50 35.0 3.55e-01 86.0% 76.0%
D2 medium residues 103-190
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s7oB00 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 0.74 66.0 6.24e-01 98.9% 81.9%
5fgmA00 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 0.73 52.0 5.89e-01 77.3% 100.0%
1a04A02 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 0.70 44.0 4.66e-01 71.6% 71.2%
2w7nA00 1.10.10.2690 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.65 48.0 4.71e-01 81.8% 72.3%
5f64A02 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 0.62 44.0 4.73e-01 72.7% 85.3%
1p4wA00 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 0.62 43.0 4.36e-01 73.9% 72.4%
5kbwB00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.58 45.0 3.74e-01 87.5% 88.9%
3py8A04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.55 42.0 3.55e-01 80.7% 68.1%
2a6cA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.52 33.0 3.48e-01 75.0% 73.7%
8dtqA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.50 38.0 3.95e-01 79.5% 93.9%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None — 0.76 65.0 6.05e-01 95.5% 74.5%
None — 0.75 66.0 6.25e-01 98.9% 81.0%
4470607 101.1.1.26 ↗ alpha arrays › HTH › HTH › Three-helical HTH › UPF0122 0.75 66.0 6.02e-01 98.9% 73.9%
4037682 101.1.1.26 ↗ alpha arrays › HTH › HTH › Three-helical HTH › UPF0122 0.75 65.0 6.22e-01 97.7% 84.0%
4683324 101.1.1.26 ↗ alpha arrays › HTH › HTH › Three-helical HTH › UPF0122 0.73 62.0 5.75e-01 95.5% 74.5%
None — 0.73 62.0 5.76e-01 95.5% 75.2%
3452676 101.1.1.267 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PF26138 0.72 50.0 4.91e-01 72.7% 83.2%
4458444 101.1.1.42 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.70 50.0 4.88e-01 73.9% 68.4%
3887530 101.1.10.41 ↗ alpha arrays › HTH › HTH › Cyclin-like › HTH_Tnp_4 0.69 48.0 4.78e-01 71.6% 84.4%
3883738 101.1.3.20 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › HTH_Tnp_4 0.69 48.0 4.77e-01 71.6% 84.4%
3892817 101.1.1.129 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_4 0.69 47.0 4.74e-01 71.6% 84.4%
4960928 101.1.3.16 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › Sigma70_r4 0.68 45.0 5.18e-01 77.3% 98.3%
5009653 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.68 47.0 5.36e-01 78.4% 96.9%
4961899 101.1.1.60 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_23 0.68 46.0 5.23e-01 73.9% 95.4%
3989117 101.1.1.129 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_4 0.68 47.0 4.53e-01 71.6% 80.0%
4970998 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.68 51.0 4.90e-01 80.7% 92.0%
4304880 101.1.1.31 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4 0.67 45.0 4.99e-01 73.9% 87.1%
3090474 4020.1.1.0 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes 0.66 50.0 4.30e-01 80.7% 90.6%
4004247 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.62 44.0 4.65e-01 75.0% 85.0%
3668668 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.61 46.0 4.19e-01 84.1% 60.0%
3693465 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.52 37.0 3.43e-01 90.9% 55.0%
4945888 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.52 35.0 3.64e-01 76.1% 76.2%