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NC_024125.2__YP_009030895.1__e112_011__00011

Bact-Vir

NC_024125.2__YP_009030895.1__e112_011__00011

Identity

Accession:
NC_024125 ↗
Kingdom:
phage

Quality

83.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Tequatrovirus› Escherichia_phage_vB_EcoM_112

TaxID: 1495285

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 8-91
PDB
Domain cluster: representative
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qf7A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 42.0 2.91e-01 95.2% 19.7%
2n6eA00 3.40.1530.20 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1805 › Protein of unknown function (DUF1491) 0.62 45.0 4.18e-01 77.4% 61.8%
2og4A01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.61 52.0 3.79e-01 96.4% 63.1%
3pp9B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 42.0 3.40e-01 77.4% 87.9%
3tt2A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 42.0 2.89e-01 77.4% 90.5%
5r0dB01 2.60.34.20 Mainly Beta › Sandwich › Substrate Binding Domain Of DNAk; Chain A, domain 1 › 0.58 41.0 3.45e-01 100.0% 44.1%
1gutA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.57 32.0 3.51e-01 96.4% 67.2%
2i7nA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 50.0 4.12e-01 100.0% 80.0%
3d3sA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 40.0 3.34e-01 76.2% 88.7%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 39.0 3.48e-01 73.8% 91.5%
2j66A01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.56 44.0 3.73e-01 85.7% 87.1%
1b9mA03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.55 30.0 3.25e-01 84.5% 59.2%
3mmyA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 43.0 2.78e-01 82.1% 75.4%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.55 49.0 4.30e-01 100.0% 75.2%
5h8yD02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.55 45.0 3.34e-01 88.1% 47.3%
3f1yA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.54 45.0 3.13e-01 95.2% 57.5%
3fdjA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.54 48.0 4.22e-01 100.0% 89.8%
6cngA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.54 48.0 4.19e-01 100.0% 89.8%
1ri6A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 42.0 2.82e-01 84.5% 98.8%
3blnA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 40.0 3.40e-01 78.6% 86.6%
5h80B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 46.0 3.37e-01 100.0% 78.9%
4k4kA02 2.60.40.2630 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 42.0 3.69e-01 86.9% 73.6%
2h3gX02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 48.0 3.87e-01 100.0% 66.7%
3k0yA02 2.60.40.2370 Mainly Beta › Sandwich › Immunoglobulin-like › NigD-like, C-terminal beta sandwich domain 0.53 42.0 3.64e-01 85.7% 82.7%
2f9wA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 47.0 4.24e-01 100.0% 100.0%
2a9sB00 3.90.950.20 Alpha Beta › Alpha-Beta Complex › Maf protein › CinA-like 0.53 45.0 3.63e-01 95.2% 78.2%
3pl5A03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.52 47.0 4.17e-01 100.0% 87.6%
4ic1D00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.52 39.0 3.02e-01 81.0% 56.8%
3jr7A03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.52 47.0 4.14e-01 100.0% 93.5%
1azpA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 31.0 3.35e-01 73.8% 72.7%
6pxcA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.52 42.0 3.93e-01 100.0% 72.1%
1u0kA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.52 38.0 3.30e-01 78.6% 75.8%
2h0eB00 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.51 42.0 3.92e-01 96.4% 92.9%
3sreA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.51 40.0 2.79e-01 89.3% 88.1%
2dirA01 3.30.2300.10 Alpha Beta › 2-Layer Sandwich › THUMP fold › THUMP superfamily 0.51 35.0 3.49e-01 83.3% 69.0%
4o5fA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 44.0 3.90e-01 100.0% 100.0%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3671921 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.70 45.0 5.32e-01 84.5% 100.0%
4473250 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.63 52.0 4.26e-01 90.5% 100.0%
3298618 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 55.0 5.13e-01 96.4% 90.5%
3966083 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.61 52.0 4.65e-01 100.0% 67.0%
3224627 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 55.0 4.18e-01 100.0% 51.6%
3666591 2484.1.1.36 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.60 51.0 3.72e-01 96.4% 56.4%
3459942 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 51.0 3.24e-01 95.2% 27.1%
3631791 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 54.0 4.34e-01 100.0% 90.6%
3328840 284.1.2.0 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases 0.59 45.0 4.51e-01 100.0% 82.4%
4456474 3019.1.1.0 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain 0.58 39.0 3.61e-01 83.3% 52.7%
3508353 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.58 53.0 3.73e-01 100.0% 70.8%
4956002 2484.4.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like 0.58 46.0 4.25e-01 86.9% 73.6%
3587578 213.1.1.31 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_10 0.56 41.0 3.45e-01 77.4% 88.2%
5071341 7581.1.1.0 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like 0.56 45.0 3.59e-01 89.3% 53.7%
4003988 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.55 33.0 3.49e-01 98.8% 65.3%
4154880 5.1.2.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_32N 0.55 41.0 2.83e-01 83.3% 81.1%
5036173 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.55 39.0 2.93e-01 75.0% 97.6%
3230187 391.1.2.9 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › Fn1_2 0.54 32.0 3.42e-01 98.8% 65.3%
3365829 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.54 40.0 2.75e-01 78.6% 46.6%
3689503 4178.1.1.0 ↗ beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.54 48.0 4.29e-01 100.0% 80.8%
4381129 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 49.0 4.11e-01 100.0% 82.7%
4645872 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 48.0 3.97e-01 100.0% 83.2%
4463270 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 48.0 4.17e-01 100.0% 89.2%
2507396 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.54 48.0 4.21e-01 100.0% 91.3%
4955135 2008.1.1.159 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Csa1 0.53 43.0 2.98e-01 89.3% 87.7%
3189694 9.1.1.33 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF1365 0.53 46.0 3.28e-01 100.0% 40.4%
3989509 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.53 36.0 3.37e-01 83.3% 53.6%
147019 3233.1.1.1 ↗ beta sandwiches › Ig-like domain in putative lipoprotein BF3042-related proteins › Ig-like domain in putative lipoprotein BF3042-related proteins › Ig-like domain in putative lipoprotein BF3042-related proteins › NigD_C 0.53 42.0 3.71e-01 85.7% 88.0%
3584519 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.53 43.0 3.66e-01 94.0% 81.3%
4945379 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.53 48.0 4.18e-01 100.0% 92.8%
4594044 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.53 47.0 3.92e-01 100.0% 86.0%
3711998 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.53 46.0 2.99e-01 100.0% 88.4%
4234891 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.52 46.0 4.04e-01 100.0% 86.2%
3587443 7523.1.1.22 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › ABC2_membrane_3 0.52 37.0 3.46e-01 85.7% 57.3%
222168 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.52 39.0 3.02e-01 81.0% 56.8%
4304211 3351.1.1.0 ↗ a/b three-layered sandwiches › Atg7 N-terminal domain-like › N-terminal domain in E1 enzyme Atg7 › N-terminal domain in E1 enzyme Atg7 0.52 41.0 3.76e-01 86.9% 81.7%
3432830 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.52 46.0 2.92e-01 100.0% 22.9%
4352045 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.52 38.0 3.80e-01 83.3% 75.6%
4945438 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.52 46.0 4.02e-01 100.0% 89.2%
4461189 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.52 46.0 4.05e-01 100.0% 92.8%
3743712 4178.1.1.1 ↗ beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › DUF5110 0.52 46.0 3.95e-01 98.8% 76.7%
3929265 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.52 45.0 3.92e-01 100.0% 85.9%
3622516 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.51 38.0 3.55e-01 81.0% 100.0%
3795541 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 38.0 3.53e-01 81.0% 100.0%
4590112 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.51 46.0 3.90e-01 100.0% 82.2%
3820308 323.1.1.15 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › WS_DGAT_C 0.50 42.0 3.26e-01 96.4% 64.3%
5081645 7528.1.1.1 ↗ a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › PGM_PMM_I 0.50 39.0 3.48e-01 96.4% 56.9%
3988804 3414.1.1.0 ↗ beta sandwiches › A putative surface protein › A putative surface protein › A putative surface protein 0.50 34.0 3.61e-01 71.4% 97.3%
4966910 7518.1.1.6 ↗ a/b three-layered sandwiches › PK C-terminal domain-like › PK C-terminal domain-like › PK C-terminal domain-like › DacZ_A 0.50 41.0 3.69e-01 91.7% 80.0%
3991271 1.1.9.33 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › PUA_NSUN2 0.50 40.0 4.16e-01 100.0% 92.5%