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NC_009813.1__YP_001468709.1__LiPB054_gp05__00005

Bact-Vir

NC_009813.1__YP_001468709.1__LiPB054_gp05__00005

Identity

Accession:
NC_009813 ↗
Kingdom:
phage

Quality

92.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_B054

TaxID: 330397

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 4-55
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xtfA00 3.90.1240.10 Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" 0.79 70.0 4.06e-01 100.0% 33.5%
2mjmA00 1.10.533.20 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › 0.67 49.0 3.98e-01 88.5% 40.6%
1dc1A02 1.10.238.90 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Restriction endonuclease BsobI, helical domain 0.62 43.0 3.60e-01 73.1% 50.0%
1khcA02 1.10.720.50 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › PWWP, helical domain 0.61 45.0 4.14e-01 80.8% 65.2%
7x0fB01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.60 43.0 3.81e-01 75.0% 94.5%
3ic9A02 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.59 40.0 3.67e-01 71.2% 92.9%
1a62A01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.58 43.0 4.61e-01 78.8% 93.5%
1j8yF01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.58 45.0 3.94e-01 90.4% 74.4%
3lbxB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 46.0 3.63e-01 88.5% 82.2%
7po9A01 3.40.1800.20 Alpha Beta › 3-Layer(aba) Sandwich › His-Me finger endonuclease fold › 0.57 49.0 4.22e-01 100.0% 76.7%
6y6hA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.57 45.0 3.30e-01 98.1% 38.5%
1kyoF00 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.56 38.0 3.45e-01 71.2% 90.5%
3gzfD00 1.10.150.420 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Coronavirus nonstructural protein 4 C-terminus 0.56 40.0 3.34e-01 76.9% 69.2%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.56 42.0 3.08e-01 82.7% 29.7%
1xt9A00 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.56 45.0 3.10e-01 94.2% 27.9%
4yshA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 46.0 3.14e-01 100.0% 87.1%
3u4qA02 1.10.274.50 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › 0.55 46.0 3.43e-01 100.0% 84.0%
1lvlA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 46.0 3.12e-01 98.1% 91.7%
1fp1D02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 41.0 2.65e-01 80.8% 80.0%
3if9A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 46.0 3.08e-01 100.0% 92.9%
1noyB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 46.0 3.06e-01 100.0% 92.0%
2v4jA01 6.10.140.1420 Special › Helix non-globular › Helix Hairpins › 0.53 37.0 3.54e-01 76.9% 96.8%
4olsA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.52 40.0 2.72e-01 86.5% 23.2%
2fekA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 41.0 3.15e-01 100.0% 89.8%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3699757 632.18.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.75 57.0 5.18e-01 88.5% 61.4%
4010451 3788.1.1.15 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › PF27202 0.71 56.0 5.01e-01 88.5% 81.3%
3622578 604.28.1.1 ↗ alpha bundles › Spectrin repeat-like › E3 ubiquitin-protein ligase SHPRH second helical domain › E3 ubiquitin-protein ligase SHPRH second helical domain › SHPRH_helical-2nd 0.65 48.0 3.16e-01 82.7% 67.5%
3928457 185.1.3.1 ↗ alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › GDNF receptor › GDNF 0.64 51.0 4.13e-01 84.6% 87.8%
3557240 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.62 50.0 3.10e-01 88.5% 18.3%
3412323 377.1.1.18 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-AD 0.62 54.0 4.82e-01 100.0% 78.7%
3839004 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.61 49.0 4.15e-01 90.4% 74.4%
4458167 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.60 42.0 3.06e-01 76.9% 29.1%
4423612 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 50.0 3.40e-01 96.2% 73.0%
5069771 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.59 46.0 3.38e-01 84.6% 82.2%
3894267 185.1.3.1 ↗ alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › GDNF receptor › GDNF 0.56 49.0 3.98e-01 96.2% 84.2%
3505170 3105.1.1.0 ↗ a+b three layers › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related 0.55 44.0 3.12e-01 90.4% 33.7%
4999971 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.54 41.0 3.37e-01 92.3% 46.7%
5005271 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.54 47.0 3.36e-01 100.0% 88.6%
5076474 2007.2.2.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Phosphotyrosine protein phosphatases I-like › LMWPc 0.54 43.0 3.25e-01 100.0% 92.9%
4652526 102.1.1.27 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_5 0.53 38.0 3.50e-01 80.8% 85.3%
3389798 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.53 40.0 3.68e-01 82.7% 80.0%
3967487 4168.1.1.1 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › HAMP 0.53 45.0 4.27e-01 96.2% 81.7%
3373978 5055.1.1.0 ↗ extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.51 36.0 3.11e-01 75.0% 88.9%