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NC_024392.1__YP_009045153.1__LP114_099__00098

Bact-Vir

NC_024392.1__YP_009045153.1__LP114_099__00098

Identity

Accession:
NC_024392 ↗
Kingdom:
phage

Quality

77.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Homburgvirus› Listeria_phage_LP-114

TaxID: 1458857

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 7-89
PDB
D2 high residues 104-231
PDB
Domain cluster: rep: MN830256.1__QHJ74974.1__X__00016__D16-151
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF10651.16 best BppU_N 53.9 2.40e-14 100.0% 81.2%
D3 high residues 304-399
PDB
Domain cluster: rep: MW960037.1__QWY83581.1__X__00027__D159-241
D4 high residues 420-518
PDB
Domain cluster: rep: KC847113.1__AGK88050.1__PBP180_0035__00035__D18-110
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7wa9A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.60 47.0 4.19e-01 83.8% 62.4%
1a87A01 3.30.1120.60 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Colicin 0.58 40.0 4.11e-01 84.8% 73.2%
2m7oA00 3.10.450.400 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Uncharacterised protein PF15513, DUF4651 0.57 36.0 4.07e-01 70.7% 88.6%
2eigA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 46.0 3.55e-01 91.9% 83.0%
1eurA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.54 48.0 3.30e-01 100.0% 63.2%
4bboA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.54 46.0 4.42e-01 99.0% 81.4%
4obiA00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.54 36.0 3.84e-01 82.8% 79.3%
3otlA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 42.0 3.68e-01 85.9% 62.1%
1ohfA03 2.60.270.70 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › 0.52 44.0 3.96e-01 93.9% 70.2%
6x05A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 45.0 3.11e-01 100.0% 51.2%
2v43A01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.51 35.0 2.93e-01 70.7% 42.1%
3mx7A00 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.51 39.0 4.06e-01 80.8% 91.1%
4jcwA02 2.60.40.760 Mainly Beta › Sandwich › Immunoglobulin-like › Expansin, cellulose-binding-like domain 0.51 35.0 3.71e-01 72.7% 93.3%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2452960 520.1.1.0 ↗ beta sandwiches › gp9 N-terminal domain-like › gp9 N-terminal domain-related › gp9 N-terminal domain-related 0.80 68.0 7.18e-01 93.9% 100.0%
4978331 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.69 38.0 4.38e-01 77.8% 74.3%
3231343 77.1.1.10 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › PF28998 0.65 43.0 3.95e-01 100.0% 51.5%
3282714 331.3.1.11 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc2 0.60 48.0 4.27e-01 85.9% 62.5%
3707862 79.1.1.0 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.59 44.0 4.87e-01 99.0% 97.5%
3703649 292.2.1.0 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.59 43.0 4.78e-01 99.0% 96.2%
5028935 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 37.0 4.31e-01 70.7% 91.4%
4017784 5.1.3.172 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PF26607 0.57 51.0 3.61e-01 100.0% 54.9%
3587129 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.56 36.0 4.19e-01 70.7% 96.9%
3695223 5.1.4.515 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF26607 0.56 50.0 3.41e-01 100.0% 68.2%
4974811 5.1.3.172 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PF26607 0.55 49.0 3.43e-01 100.0% 84.5%
4927158 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 48.0 3.13e-01 100.0% 60.2%
4974812 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 48.0 3.43e-01 99.0% 58.7%
3992231 12.1.1.102 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_30 0.55 47.0 3.05e-01 98.0% 34.4%
4978599 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 50.0 3.36e-01 100.0% 53.2%
5059043 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 46.0 3.21e-01 100.0% 62.0%
3739521 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.52 37.0 3.78e-01 75.8% 93.0%
D5 high residues 522-630
PDB
Domain cluster: rep: OR521085.1__WNO28334.1__SEA_PSONYX_24__00024__D30-132
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF27455.1 best YomR_C 27.2 4.40e-06 93.6% 80.8%
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2f0cA02 2.60.40.1830 Mainly Beta › Sandwich › Immunoglobulin-like › Phage tail base-plate Siphoviridae RBP, head domain 0.79 68.0 6.95e-01 100.0% 96.2%
2bseA00 2.60.40.1830 Mainly Beta › Sandwich › Immunoglobulin-like › Phage tail base-plate Siphoviridae RBP, head domain 0.77 67.0 6.79e-01 100.0% 94.4%
2fsdA00 2.60.40.2460 Mainly Beta › Sandwich › Immunoglobulin-like › Phage bIL170 RBP, head domain 0.77 70.0 7.06e-01 100.0% 98.2%
1kacA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.73 66.0 5.52e-01 100.0% 96.2%
2wstA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.73 65.0 5.58e-01 100.0% 97.7%
6g47A00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.71 64.0 5.54e-01 100.0% 98.2%
1h7zA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.71 64.0 5.33e-01 100.0% 97.9%
1y8cA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.67 32.0 4.16e-01 99.1% 81.7%
2bzvA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.63 58.0 5.22e-01 100.0% 97.9%
2eabB03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.62 46.0 4.45e-01 98.2% 69.7%
2xdhA00 2.60.40.680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 47.0 4.36e-01 89.0% 63.8%
4pqqA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 49.0 4.43e-01 89.9% 80.1%
2ylkA00 2.60.40.710 Mainly Beta › Sandwich › Immunoglobulin-like › Endoglucanase-like 0.60 49.0 4.52e-01 89.9% 73.8%
3zn6A02 2.60.40.3410 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 42.0 4.60e-01 72.5% 100.0%
1o59A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 49.0 4.56e-01 89.9% 90.6%
1iarB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 42.0 4.48e-01 100.0% 84.4%
3ammA00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.59 53.0 4.08e-01 100.0% 96.9%
1w8oA03 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 50.0 4.59e-01 100.0% 97.9%
2v72A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 50.0 4.69e-01 100.0% 79.6%
2n59A00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 38.0 3.97e-01 74.3% 82.2%
3mwxA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 46.0 3.39e-01 100.0% 92.2%
4ok4A02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 46.0 3.28e-01 100.0% 78.1%
3vy8X00 2.40.160.10 Mainly Beta › Beta Barrel › Porin › Porin 0.53 43.0 3.12e-01 90.8% 44.3%
4uxuA00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.52 42.0 3.49e-01 89.0% 61.0%
1v0fB03 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.52 37.0 3.99e-01 74.3% 97.6%
6f90A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 45.0 3.47e-01 100.0% 76.0%
1lf6A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 44.0 3.43e-01 100.0% 76.2%
3zfnA02 2.30.140.40 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Pestivirus Npro endopeptidase C53, interaction domain 0.51 26.0 3.33e-01 80.7% 91.2%
2grgA01 3.40.1840.10 Alpha Beta › 3-Layer(aba) Sandwich › Profilin-like › YNR034W-A-like 0.50 30.0 3.28e-01 82.6% 73.5%
1vr8A00 3.40.1000.20 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › TM1622-like 0.50 38.0 3.59e-01 81.7% 77.0%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3588403 5092.1.1.0 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins 0.85 75.0 7.75e-01 100.0% 98.1%
961561 5092.1.1.4 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Caudo_bapla_RBP 0.78 68.0 6.96e-01 100.0% 97.1%
184600 5092.1.1.4 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Caudo_bapla_RBP 0.77 70.0 7.06e-01 100.0% 98.2%
1156585 5092.1.1.4 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Caudo_bapla_RBP 0.77 67.0 6.65e-01 100.0% 90.3%
2491361 5092.1.1.0 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins 0.68 60.0 5.72e-01 100.0% 98.5%
3783233 4081.1.1.7 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Ribophorin_I 0.65 54.0 4.46e-01 90.8% 50.8%
1487334 5092.1.1.7 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Fibre_HD 0.64 56.0 5.50e-01 100.0% 91.4%
3876068 391.1.1.9 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › EGF1_RECK 0.60 28.0 3.78e-01 81.7% 92.0%
5070692 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 43.0 4.54e-01 99.1% 87.4%
4948100 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.59 52.0 3.93e-01 100.0% 92.9%
4960956 12.5.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related 0.59 51.0 4.51e-01 96.3% 78.8%
4816119 12.1.1.25 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Fucosidase_C 0.58 50.0 5.06e-01 97.2% 95.5%
1318480 10.32.1.2 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › F5_F8_type_C 0.57 50.0 4.59e-01 100.0% 99.3%
3628177 10.32.1.11 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › ANAPC10 0.56 46.0 4.01e-01 90.8% 78.3%
4978194 7072.1.1.0 ↗ beta sandwiches › N-terminal half of TgpA periplasmic domain › N-terminal half of TgpA periplasmic domain › N-terminal half of TgpA periplasmic domain 0.56 47.0 4.31e-01 93.6% 93.3%
3931830 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.55 44.0 3.80e-01 88.1% 62.2%
3492090 11.1.3.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Cu,Zn superoxide dismutase-like › Sod_Cu 0.54 45.0 4.12e-01 100.0% 66.7%
3611958 11.1.1.105 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Coatamer_beta_C 0.54 43.0 4.05e-01 89.9% 71.1%
3890932 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.54 46.0 3.34e-01 98.2% 76.2%
3873815 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 38.0 3.63e-01 100.0% 61.5%
4978843 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 47.0 4.50e-01 100.0% 86.4%
4398429 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.52 33.0 3.71e-01 87.2% 86.3%
4609835 12.3.1.3 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Aldose_epim 0.51 44.0 3.32e-01 100.0% 97.0%
3698469 225.1.1.7 ↗ 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_3 0.50 43.0 3.51e-01 100.0% 56.5%
D6 medium residues 240-303
PDB
Domain cluster: representative