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NC_025470.1__YP_009104170.1__S140_172__00169

Bact-Vir

NC_025470.1__YP_009104170.1__S140_172__00169

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

72.9 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 4-62
PDB
D2 high residues 68-119
PDB
CATH (61)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2gukA00 3.30.2190.10 Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like 0.67 51.0 4.13e-01 88.5% 45.0%
1gcyA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.65 47.0 4.67e-01 78.8% 75.0%
2jnaA01 3.30.1660.10 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › Flavin-binding protein dodecin 0.65 46.0 4.24e-01 76.9% 79.7%
3dmgA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 52.0 3.69e-01 94.2% 30.5%
7ovuA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.64 53.0 3.67e-01 98.1% 86.5%
3dtnA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.63 50.0 3.56e-01 94.2% 31.0%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 44.0 3.85e-01 76.9% 61.8%
1j4wA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.63 45.0 4.07e-01 76.9% 68.9%
2oh1C00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 53.0 3.75e-01 98.1% 97.1%
2b3tA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 50.0 3.50e-01 94.2% 28.6%
4hl9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 44.0 3.69e-01 76.9% 56.4%
2hqyA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 49.0 3.82e-01 94.2% 43.1%
4bmhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 51.0 3.54e-01 100.0% 27.7%
3fxtA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 51.0 4.33e-01 96.2% 57.8%
3v97A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.61 49.0 3.50e-01 94.2% 29.6%
5hmaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.60 47.0 4.00e-01 86.5% 82.8%
2wnyA00 3.30.1440.10 Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 0.60 42.0 3.19e-01 76.9% 35.0%
1dp7P00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 47.0 4.32e-01 94.2% 93.4%
1u6mA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 49.0 3.42e-01 96.2% 31.7%
2anrA02 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.59 42.0 3.80e-01 76.9% 65.3%
1ej6A05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 43.0 3.63e-01 80.8% 61.1%
3fixA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 49.0 3.58e-01 100.0% 33.9%
1f0xA04 3.30.1370.20 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › D-lactate dehydrogenase, cap domain, subdomain 2 0.59 41.0 3.63e-01 76.9% 55.3%
4dzrA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 46.0 3.41e-01 94.2% 34.4%
5fiiB00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 41.0 3.70e-01 76.9% 61.5%
2qb7B02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.58 43.0 3.19e-01 80.8% 37.1%
2f9jA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 40.0 3.62e-01 76.9% 60.0%
6lpnA04 3.30.70.2740 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 40.0 3.46e-01 76.9% 50.5%
1qzzA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 45.0 3.32e-01 96.2% 50.9%
4fvaC00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.57 43.0 2.83e-01 94.2% 17.9%
4avaA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 47.0 3.36e-01 100.0% 82.5%
5h20A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 47.0 3.89e-01 100.0% 66.0%
3vmnA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 44.0 3.29e-01 88.5% 59.2%
3fzqA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.56 45.0 3.60e-01 92.3% 97.4%
6v3pD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 41.0 3.44e-01 82.7% 58.6%
4nb5B01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 46.0 4.02e-01 100.0% 80.0%
2yvsA02 3.30.70.2560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 38.0 3.72e-01 76.9% 66.1%
1s3jA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 43.0 4.09e-01 92.3% 98.4%
2zihC00 1.10.3630.10 Mainly Alpha › Orthogonal Bundle › yeast vps74-n-term truncation variant fold › yeast vps74-n-term truncation variant domain like 0.55 46.0 2.95e-01 100.0% 51.6%
1ve4A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.55 39.0 3.07e-01 86.5% 33.9%
4tshB01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 40.0 2.94e-01 86.5% 53.8%
1r6vA02 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.54 38.0 3.51e-01 80.8% 57.7%
4xrfA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 43.0 3.35e-01 100.0% 43.7%
2x3gA00 3.30.70.1910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 40.0 3.24e-01 84.6% 46.6%
2bv6A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 43.0 3.39e-01 100.0% 55.9%
3r0aA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 43.0 3.50e-01 100.0% 61.7%
2dqlA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 42.0 3.44e-01 96.2% 64.3%
3en9A03 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 38.0 3.49e-01 78.8% 89.0%
2yweA03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.53 37.0 3.32e-01 76.9% 61.0%
5dymA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 44.0 3.73e-01 100.0% 70.8%
2jtvA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 45.0 4.22e-01 100.0% 78.5%
1iugA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 39.0 3.20e-01 84.6% 55.9%
6bq9A02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.53 37.0 3.21e-01 78.8% 57.4%
2qmwA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 38.0 3.35e-01 86.5% 59.1%
6abqB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 43.0 3.56e-01 100.0% 65.1%
2pt7G02 3.30.1370.180 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.52 37.0 3.59e-01 86.5% 80.6%
3pqvC01 3.65.10.20 Alpha Beta › Alpha-beta prism › UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain › RNA 3'-terminal phosphate cyclase domain 0.51 40.0 2.75e-01 100.0% 94.5%
4ejoA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 43.0 3.49e-01 100.0% 62.5%
3i24B00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.51 38.0 2.95e-01 86.5% 54.7%
3gz7B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.04e-01 76.9% 59.2%
2oikA00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.50 39.0 3.03e-01 94.2% 79.1%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1839973 877.1.1.5 a+b duplicates or obligate multimers › gp11/gp12 receptor-binding domain › gp11/gp12 receptor-binding domain › gp11/gp12 receptor-binding domain › Gp10_C 0.82 73.0 4.78e-01 98.1% 75.5%
3996681 389.2.1.3 few secondary structure elements › EGF-like › Serine protease inhibitors › Serine protease inhibitors › TIL_2 0.69 50.0 4.92e-01 86.5% 72.7%
3954670 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.69 56.0 3.82e-01 94.2% 36.0%
3324732 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.69 48.0 3.98e-01 76.9% 41.1%
3497652 864.1.1.0 a+b two layers › DLC › DLC › DLC 0.67 45.0 3.92e-01 76.9% 43.5%
4496868 304.7.1.4 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › S8_pro-domain 0.65 46.0 3.90e-01 76.9% 45.9%
3969288 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.64 52.0 3.80e-01 96.2% 98.2%
5028345 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.64 52.0 3.59e-01 94.2% 41.7%
3407460 328.12.1.1 a+b two layers › IF3-like › IF3-like domain in Nudix hydrolase › IF3-like domain in Nudix hydrolase › Nudix_hydro 0.63 54.0 4.37e-01 96.2% 52.0%
3522202 11.1.1.589 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › NUP210_Ig 0.63 46.0 3.19e-01 80.8% 26.0%
1978 12.1.1.8 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › AMT4_dom_C 0.63 48.0 4.65e-01 86.5% 90.2%
3404233 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.63 53.0 3.53e-01 100.0% 25.6%
3598932 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.62 48.0 3.93e-01 88.5% 81.0%
3853324 328.12.1.1 a+b two layers › IF3-like › IF3-like domain in Nudix hydrolase › IF3-like domain in Nudix hydrolase › Nudix_hydro 0.62 53.0 4.30e-01 96.2% 52.0%
3706300 2492.1.1.2 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.62 48.0 3.18e-01 84.6% 87.6%
4344201 864.1.1.0 a+b two layers › DLC › DLC › DLC 0.61 43.0 3.70e-01 76.9% 51.1%
3997333 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.61 42.0 3.67e-01 75.0% 70.0%
3801762 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.61 42.0 4.12e-01 75.0% 70.0%
5013315 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.61 52.0 3.73e-01 100.0% 32.9%
4324707 2003.1.5.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.61 49.0 3.19e-01 94.2% 19.6%
3298862 304.5.1.1 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.61 42.0 3.18e-01 76.9% 55.0%
5076899 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.60 50.0 3.49e-01 94.2% 46.3%
5000808 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.60 44.0 4.51e-01 84.6% 84.0%
4999416 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.60 52.0 3.71e-01 100.0% 84.4%
3989733 213.1.1.25 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.60 51.0 3.67e-01 100.0% 98.8%
4927527 304.5.1.1 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.60 44.0 3.55e-01 82.7% 57.3%
5064968 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.60 50.0 3.82e-01 98.1% 66.9%
3516764 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.59 41.0 4.04e-01 76.9% 71.7%
169936 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.59 49.0 3.62e-01 100.0% 35.2%
5018285 213.1.1.25 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.58 49.0 3.97e-01 100.0% 53.6%
5019208 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.58 49.0 3.65e-01 100.0% 37.9%
4404322 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.58 40.0 3.52e-01 76.9% 45.9%
4167096 2003.1.1.61 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › KR 0.58 47.0 2.82e-01 96.2% 17.6%
4948149 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 48.0 3.87e-01 100.0% 58.2%
3969012 101.1.2.485 alpha arrays › HTH › HTH › winged helix domain › DUF2513 0.55 47.0 4.00e-01 100.0% 71.1%
3607708 4178.1.1.0 beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.55 42.0 2.98e-01 88.5% 45.0%
3308403 601.23.1.1 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.54 42.0 2.61e-01 88.5% 17.9%
165944 101.1.2.202 alpha arrays › HTH › HTH › winged helix domain › DUF3860-like 0.53 45.0 4.22e-01 100.0% 78.5%
5062261 101.1.2.892 alpha arrays › HTH › HTH › winged helix domain › ArsR 0.53 43.0 3.65e-01 100.0% 66.0%
4071195 206.1.1.11 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.53 37.0 2.25e-01 76.9% 42.3%
5062596 205.1.1.130 a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_8 0.52 36.0 2.95e-01 76.9% 50.4%
4959674 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.51 41.0 3.14e-01 96.2% 99.3%
4045579 2003.1.5.25 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GidB 0.51 38.0 2.79e-01 92.3% 24.6%
3472374 11.1.1.12 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Filamin 0.51 36.0 3.08e-01 82.7% 55.2%
3220501 864.1.1.0 a+b two layers › DLC › DLC › DLC 0.50 35.0 3.12e-01 76.9% 48.2%