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NC_019486.1__YP_007003219.1__F374_gp19__00019

Bact-Vir

NC_019486.1__YP_007003219.1__F374_gp19__00019

Identity

Accession:
NC_019486 ↗
Kingdom:
phage

Quality

93.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lafunavirus› Lactobacillus_phage_LF1

TaxID: 947980

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 high residues 3-72
PDB
Domain cluster: rep: MG788324.1__AVH85811.1__X__00068__D74-140
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.72 44.0 4.65e-01 90.0% 68.3%
2rsxA00 3.10.450.420 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 45.0 3.43e-01 100.0% 31.4%
4u13A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 42.0 3.64e-01 98.6% 43.1%
1ni9A01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.64 40.0 3.12e-01 70.0% 29.8%
3kxtA00 2.30.30.610 Mainly Beta › Roll › SH3 type barrels. › Chromatin protein Cren7 0.64 37.0 4.09e-01 80.0% 71.4%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.62 45.0 3.81e-01 100.0% 44.0%
1ut7B01 2.170.150.80 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › NAC domain 0.62 45.0 3.74e-01 94.3% 44.0%
2v1oB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.60 38.0 3.05e-01 74.3% 29.7%
2a1rB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 52.0 3.48e-01 100.0% 75.0%
8fkmA01 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.60 48.0 3.79e-01 92.9% 61.6%
2fggA01 3.30.160.240 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Rv1738 0.59 47.0 4.64e-01 100.0% 82.7%
4ebrA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.59 46.0 3.61e-01 85.7% 65.6%
2lpuA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.59 44.0 3.61e-01 85.7% 66.9%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.58 50.0 4.48e-01 100.0% 66.7%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.58 49.0 4.06e-01 95.7% 83.2%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.58 46.0 4.46e-01 100.0% 78.5%
4ydzA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 45.0 3.70e-01 88.6% 45.2%
3mg1B02 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 42.0 3.55e-01 100.0% 44.8%
1wnhA02 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 42.0 3.52e-01 98.6% 45.0%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 49.0 4.83e-01 100.0% 91.9%
1yvuA04 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 49.0 3.54e-01 100.0% 94.4%
4pkcC00 6.20.90.20 Special › Other non-globular › SH3 type barrels. › Benzylsuccinate synthase gamma subunit 0.56 33.0 3.94e-01 81.4% 100.0%
1gkuB07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.55 44.0 3.90e-01 91.4% 59.8%
3en2A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 48.0 4.40e-01 100.0% 82.4%
3en8A01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 39.0 3.41e-01 100.0% 48.2%
3mcrA00 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.54 42.0 3.33e-01 87.1% 46.1%
2g7uC02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 40.0 3.08e-01 94.3% 32.0%
3hk4A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 39.0 3.36e-01 98.6% 47.5%
3r4kA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.52 43.0 3.29e-01 97.1% 37.4%
1pv1A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 47.0 3.10e-01 100.0% 51.7%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 46.0 3.10e-01 98.6% 27.7%
3ub1D02 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 36.0 3.24e-01 98.6% 47.4%
4o8sA01 3.10.450.620 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › JHP933, nucleotidyltransferase-like core domain 0.51 37.0 3.11e-01 97.1% 43.2%
4qclA01 2.40.50.730 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 43.0 4.06e-01 100.0% 75.6%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.51 38.0 2.72e-01 82.9% 38.1%
1wchA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.51 45.0 2.93e-01 100.0% 22.1%
2covG00 2.60.40.2450 Mainly Beta › Sandwich › Immunoglobulin-like › Beta-1,3-xylanase, CBM31 domain 0.51 38.0 3.55e-01 81.4% 78.4%
3wasA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.50 42.0 2.73e-01 100.0% 24.4%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4135153 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.74 53.0 5.18e-01 100.0% 69.3%
5067760 283.1.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase 0.73 41.0 3.77e-01 70.0% 43.3%
3352475 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.72 59.0 5.85e-01 100.0% 85.3%
2321284 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.70 42.0 3.54e-01 94.3% 37.7%
3472467 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.70 54.0 5.28e-01 95.7% 77.3%
4004011 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.69 50.0 4.34e-01 100.0% 49.1%
5023443 330.4.1.0 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 0.68 47.0 4.85e-01 100.0% 76.9%
3260045 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.67 45.0 4.42e-01 98.6% 64.0%
1149748 2484.1.1.45 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › CAF1 0.67 48.0 3.84e-01 75.7% 81.6%
3466675 2484.1.1.45 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › CAF1 0.65 49.0 3.85e-01 81.4% 82.7%
4661118 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.64 56.0 4.70e-01 100.0% 93.6%
4048220 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.64 51.0 4.91e-01 100.0% 75.0%
3488611 383.1.2.0 ↗ few secondary structure elements › Defensin-like › Defensin-related › Laterosporulin 0.64 37.0 4.57e-01 71.4% 100.0%
4086062 5.1.3.20 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PD40 0.64 44.0 2.82e-01 100.0% 14.7%
4979306 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.63 47.0 4.61e-01 100.0% 72.0%
3221974 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.63 45.0 3.99e-01 98.6% 50.5%
1933323 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.63 52.0 3.31e-01 91.4% 94.8%
3217507 243.1.1.98 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF5382_C 0.63 39.0 3.30e-01 70.0% 37.7%
3483729 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.63 54.0 4.57e-01 98.6% 95.8%
3389979 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.63 51.0 4.25e-01 88.6% 51.7%
4175367 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 49.0 4.56e-01 97.1% 66.7%
3180828 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.62 55.0 4.03e-01 100.0% 44.7%
5030187 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.62 44.0 4.27e-01 100.0% 67.9%
3269932 5.1.5.27 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › APEH_N 0.62 51.0 3.07e-01 90.0% 98.3%
5056218 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.60 41.0 4.12e-01 98.6% 70.0%
5047301 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 50.0 4.60e-01 100.0% 71.1%
4946229 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.60 46.0 3.49e-01 84.3% 34.5%
3709133 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 47.0 3.96e-01 85.7% 60.0%
4638787 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.60 48.0 4.60e-01 100.0% 76.2%
5062717 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.60 40.0 3.40e-01 70.0% 43.5%
4955652 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.59 49.0 3.10e-01 91.4% 96.3%
3255739 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.59 45.0 4.58e-01 85.7% 82.9%
3687369 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.59 43.0 3.89e-01 90.0% 56.0%
4984221 5.1.8.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › putative conserved lipoprotein NT01CX_1156 0.58 39.0 3.17e-01 100.0% 33.8%
3937109 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.57 41.0 2.72e-01 91.4% 16.9%
3827488 319.1.1.15 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › PF27746 0.57 50.0 4.34e-01 98.6% 81.8%
4865157 243.1.1.17 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › TpcC 0.57 43.0 3.69e-01 92.9% 50.0%
4017880 3385.1.1.0 ↗ beta barrels › Allergen Alt a 1 › Allergen Alt a 1 › Allergen Alt a 1 0.56 48.0 3.85e-01 95.7% 67.1%
3996931 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 37.0 3.88e-01 70.0% 89.2%
3592202 2003.6.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like 0.56 49.0 3.23e-01 100.0% 39.3%
1822815 6173.1.1.1 ↗ beta barrels › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 › GP120 0.55 36.0 4.19e-01 84.3% 100.0%
4220705 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.55 42.0 3.12e-01 81.4% 38.9%
3505182 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 45.0 4.37e-01 90.0% 88.7%
3798397 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.55 35.0 3.17e-01 70.0% 45.0%
3601320 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.55 45.0 3.96e-01 91.4% 62.0%
4880181 1061.1.1.1 ↗ a+b two layers › gp120 inner domain › gp120 inner domain › gp120 inner domain › GP120 0.54 37.0 3.02e-01 81.4% 36.6%
3883616 378.1.1.1 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › Endonuclease_NS 0.54 48.0 3.23e-01 100.0% 29.1%
3175183 868.1.1.4 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › VTC 0.54 47.0 3.11e-01 100.0% 43.5%
4839875 1061.1.1.1 ↗ a+b two layers › gp120 inner domain › gp120 inner domain › gp120 inner domain › GP120 0.53 40.0 4.33e-01 85.7% 100.0%
3914493 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 47.0 2.74e-01 98.6% 12.0%
3867704 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.52 47.0 3.02e-01 98.6% 23.2%
4049252 11.1.4.102 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SOP4 0.52 44.0 3.45e-01 92.9% 44.7%
3907410 378.1.1.1 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › Endonuclease_NS 0.52 46.0 3.15e-01 100.0% 29.0%
3992783 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 36.0 2.56e-01 100.0% 21.3%
5047088 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.51 42.0 3.12e-01 98.6% 53.6%
3315173 243.3.1.46 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › SWIM 0.51 41.0 3.52e-01 90.0% 56.5%
3405822 220.1.1.43 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SIN1_PH 0.50 38.0 3.09e-01 84.3% 51.7%
3634542 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.50 41.0 3.26e-01 97.1% 46.7%