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NC_024392.1__YP_009045092.1__LP114_038__00037

Bact-Vir

NC_024392.1__YP_009045092.1__LP114_038__00037

Identity

Accession:
NC_024392 ↗
Kingdom:
phage

Quality

58.3 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 72-148
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.82 57.0 5.42e-01 71.4% 78.4%
2cmrA00 1.20.58.1860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 61.0 4.46e-01 83.1% 87.0%
1x0tA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.73 47.0 5.22e-01 89.6% 83.6%
4cb8A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.71 62.0 3.76e-01 96.1% 26.2%
4lunU00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.71 59.0 3.82e-01 89.6% 21.9%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 59.0 5.75e-01 90.9% 82.1%
5yixA00 1.10.601.10 Mainly Alpha › Orthogonal Bundle › RNA Polymerase Primary Sigma Factor › RNA Polymerase Primary Sigma Factor 0.70 61.0 3.95e-01 93.5% 47.5%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 58.0 5.21e-01 89.6% 78.1%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 58.0 5.19e-01 89.6% 86.5%
1dn1B00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 58.0 4.10e-01 92.2% 63.5%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 58.0 5.83e-01 90.9% 91.0%
2pusA04 6.10.140.300 Special › Helix non-globular › Helix Hairpins › 0.68 54.0 4.82e-01 85.7% 68.5%
3cbuA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 61.0 5.04e-01 100.0% 79.9%
1d8cA03 1.20.1220.12 Mainly Alpha › Up-down Bundle › Malate Synthase G; Chain: A; Domain 4 › Malate synthase, domain III 0.68 56.0 4.76e-01 94.8% 82.2%
1y1uA01 1.20.1050.20 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › STAT transcription factor, all-alpha domain 0.67 61.0 4.43e-01 97.4% 77.4%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.66 60.0 5.01e-01 100.0% 87.5%
3lszA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.65 57.0 4.92e-01 100.0% 79.2%
7miqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.65 58.0 5.16e-01 100.0% 93.6%
4it4A02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.64 50.0 4.76e-01 93.5% 71.4%
2cwoA01 1.20.58.1200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RNA silencing suppressor P21, N-terminal domain 0.64 49.0 5.06e-01 88.3% 86.5%
7bqiA01 1.20.58.900 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain 0.64 59.0 4.63e-01 100.0% 91.4%
2ra1A01 1.20.58.790 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 49.0 4.59e-01 89.6% 77.6%
1lujB01 1.10.10.490 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Beta-catenin-interacting ICAT 0.61 35.0 4.08e-01 84.4% 81.1%
3hdjA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 40.0 3.12e-01 100.0% 30.4%
3nrhA00 1.20.120.1550 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Protein of unknown function DUF5063 0.59 50.0 4.04e-01 96.1% 79.7%
2cz2A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 51.0 4.44e-01 100.0% 79.4%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.59 51.0 4.00e-01 100.0% 54.6%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.58 43.0 4.36e-01 89.6% 77.2%
3fr3B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 50.0 4.45e-01 100.0% 86.1%
8a0rA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 49.0 4.24e-01 100.0% 80.8%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.57 43.0 3.93e-01 94.8% 60.2%
3hi0A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 48.0 4.26e-01 100.0% 85.5%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 47.0 3.88e-01 97.4% 92.4%
3u7rA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.54 47.0 3.63e-01 100.0% 74.2%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 44.0 4.01e-01 94.8% 88.8%
7uvpA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 42.0 3.00e-01 92.2% 44.9%
1hc7A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 39.0 2.72e-01 80.5% 83.3%
1i7dA01 3.40.50.140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 45.0 3.67e-01 100.0% 74.4%
2yksA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.50 43.0 3.84e-01 100.0% 94.9%
2vk9A03 1.10.3730.30 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › 0.50 35.0 3.26e-01 72.7% 80.6%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3238365 109.4.1.32 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.88 62.0 3.61e-01 72.7% 11.1%
3618144 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.80 63.0 4.07e-01 81.8% 22.0%
3936188 109.4.1.32 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.79 64.0 3.72e-01 97.4% 12.1%
3695880 109.4.1.32 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.78 62.0 3.56e-01 100.0% 10.8%
3518551 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 62.0 3.97e-01 100.0% 20.6%
3941457 1203.1.2.3 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › YiaAB 0.74 58.0 4.96e-01 83.1% 65.8%
3459951 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.74 66.0 5.72e-01 93.5% 70.9%
5083776 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.74 62.0 5.77e-01 89.6% 80.0%
3704019 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.71 61.0 5.43e-01 90.9% 76.2%
4998039 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.71 63.0 5.69e-01 93.5% 72.0%
5059237 3457.1.1.3 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.70 63.0 3.96e-01 96.1% 37.8%
3704359 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 59.0 4.43e-01 89.6% 50.9%
3256821 603.1.1.99 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27021 0.70 61.0 5.19e-01 93.5% 60.8%
4091932 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.69 57.0 4.72e-01 89.6% 85.9%
3246395 603.1.1.1 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin 0.69 62.0 4.50e-01 98.7% 90.7%
5046472 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.69 57.0 5.30e-01 94.8% 72.6%
3497418 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 58.0 5.26e-01 90.9% 74.0%
4289864 601.25.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › TrmE connector domain › TrmE connector domain 0.68 63.0 4.98e-01 100.0% 70.0%
3776754 5055.1.1.0 ↗ extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.68 51.0 5.57e-01 87.0% 93.8%
3341807 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.68 55.0 4.89e-01 90.9% 61.8%
1291132 109.40.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.68 56.0 4.64e-01 94.8% 52.3%
3425147 109.4.1.1557 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_RNF123 0.67 59.0 4.44e-01 100.0% 76.4%
4971844 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.67 60.0 5.13e-01 96.1% 91.7%
3441715 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 57.0 5.02e-01 90.9% 77.3%
4025271 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 57.0 5.16e-01 90.9% 73.0%
3779360 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.67 49.0 3.81e-01 76.6% 72.5%
5030299 633.16.1.0 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like 0.67 54.0 5.38e-01 94.8% 82.5%
4988250 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.66 56.0 3.70e-01 93.5% 78.8%
5056832 3457.1.1.1 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 0.66 61.0 4.72e-01 100.0% 96.2%
3654456 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.66 50.0 3.41e-01 84.4% 71.5%
4012658 5059.1.1.0 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter 0.65 48.0 3.24e-01 80.5% 25.1%
3607638 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 54.0 3.59e-01 94.8% 41.2%
5057996 3457.1.1.1 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 0.62 57.0 4.43e-01 100.0% 96.2%
3788066 603.2.1.0 ↗ alpha bundles › STAT-like › STAT › STAT 0.62 54.0 4.14e-01 100.0% 57.8%
3938635 603.2.1.0 ↗ alpha bundles › STAT-like › STAT › STAT 0.61 52.0 4.25e-01 98.7% 89.7%
5063729 3457.1.1.1 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 0.61 55.0 4.08e-01 100.0% 100.0%
3252688 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.60 52.0 4.12e-01 98.7% 54.5%
3240455 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.60 48.0 4.62e-01 89.6% 87.8%
3577682 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.59 53.0 4.36e-01 100.0% 83.6%
5052878 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.59 53.0 4.94e-01 100.0% 94.7%
4056284 601.25.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › TrmE connector domain › TrmE connector domain › MnmE_helical 0.59 51.0 4.05e-01 100.0% 66.3%
4951522 3457.1.1.3 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.59 51.0 3.70e-01 100.0% 49.6%
4134938 601.3.1.14 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › PF27870 0.59 53.0 4.61e-01 100.0% 70.4%
3696925 196.1.1.1 ↗ alpha bundles › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › RGS 0.59 51.0 4.16e-01 100.0% 64.7%
3535566 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.58 51.0 4.42e-01 100.0% 88.8%
4075932 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.58 51.0 3.16e-01 100.0% 27.1%
3729492 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.57 50.0 4.09e-01 100.0% 82.0%
3227148 196.1.1.1 ↗ alpha bundles › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › RGS 0.57 51.0 4.07e-01 100.0% 54.2%
5028214 3457.1.1.1 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 0.57 50.0 3.74e-01 100.0% 98.0%
5044650 3457.1.1.1 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Peptidase_A24 0.56 50.0 3.96e-01 100.0% 98.1%
4600613 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.55 48.0 4.09e-01 100.0% 90.0%
4465300 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.55 38.0 3.64e-01 94.8% 62.2%
3595289 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 47.0 4.44e-01 100.0% 88.4%
3934654 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.53 44.0 3.43e-01 94.8% 52.2%
4133362 632.11.1.6 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › Yae1_N 0.52 35.0 3.31e-01 96.1% 56.8%
4934635 5065.1.1.3 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › BPD_transp_2 0.50 43.0 2.97e-01 94.8% 46.8%
D2 medium residues 1-65
PDB