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NC_049340.1__YP_009873721.1__HYO65_gp037__00037

Bact-Vir

NC_049340.1__YP_009873721.1__HYO65_gp037__00037

Identity

Accession:
NC_049340 ↗
Kingdom:
phage

Quality

77.0 mean pLDDT

3D Structure

Domains

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

D1 medium residues 1-60
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4pswA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.70 52.0 4.01e-01 86.7% 36.1%
4nesA02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.68 46.0 3.31e-01 78.3% 25.2%
2p0wA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.67 49.0 3.81e-01 85.0% 35.3%
1jhdA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.67 55.0 3.80e-01 100.0% 27.1%
1vk3A03 3.30.1330.10 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › PurM-like, N-terminal domain 0.64 50.0 3.91e-01 100.0% 37.4%
2h8lA02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.63 45.0 3.71e-01 76.7% 63.4%
5xilA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.63 50.0 3.91e-01 85.0% 46.1%
4gt8A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.63 44.0 3.42e-01 78.3% 33.1%
3s2cA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.62 53.0 3.36e-01 100.0% 20.2%
1q0sA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 46.0 3.52e-01 98.3% 33.6%
3a4lB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 47.0 3.33e-01 83.3% 27.5%
4s39A02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.62 44.0 3.51e-01 75.0% 56.0%
2gb3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.62 44.0 3.22e-01 75.0% 67.1%
1on4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 42.0 3.12e-01 81.7% 25.3%
1k4kB00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.61 52.0 3.57e-01 100.0% 27.9%
4aw7A02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.61 52.0 3.33e-01 100.0% 21.5%
2zigA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 51.0 3.46e-01 100.0% 24.6%
4wnyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.60 52.0 4.11e-01 100.0% 60.6%
4fdxB00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.59 41.0 4.01e-01 76.7% 65.6%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.59 50.0 3.84e-01 100.0% 77.6%
1nj1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.59 46.0 3.87e-01 85.0% 49.0%
2jh3A01 3.40.50.1400 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 44.0 3.42e-01 81.7% 41.5%
3cm0A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 48.0 3.56e-01 100.0% 40.8%
6bk1A02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.58 38.0 2.80e-01 86.7% 22.7%
7t85A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 44.0 3.29e-01 98.3% 31.7%
3luyA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 36.0 2.94e-01 78.3% 31.9%
3c3kA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 42.0 3.24e-01 80.0% 47.8%
6ks6Q03 3.50.7.10 Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL 0.57 43.0 3.25e-01 83.3% 40.1%
3m21F00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.57 38.0 3.73e-01 75.0% 62.7%
3id7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.56 47.0 2.96e-01 100.0% 18.9%
1ej0A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 47.0 3.46e-01 100.0% 47.2%
3ktbA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 41.0 3.49e-01 91.7% 48.1%
5hy0A01 3.30.1330.170 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Cyanuric acid hydrolase/Barbiturase, RU A 0.54 45.0 3.76e-01 98.3% 53.7%
2dlxA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 36.0 3.09e-01 83.3% 38.9%
1r26A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 32.0 2.63e-01 100.0% 31.0%
1jx6A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 45.0 3.43e-01 100.0% 41.1%
1o1yA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.52 42.0 2.90e-01 91.7% 40.0%
1zunB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 46.0 3.19e-01 100.0% 40.4%
4n03A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 41.0 3.03e-01 100.0% 31.2%
1iqcA01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.51 39.0 2.97e-01 86.7% 85.7%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5075804 2484.1.1.337 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RRXRR 0.79 63.0 4.46e-01 100.0% 28.6%
4938348 2484.1.1.25 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.75 62.0 4.47e-01 100.0% 32.7%
5066472 2006.1.3.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › Toprim 0.74 50.0 4.15e-01 78.3% 40.0%
4984062 7592.1.1.3 a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.70 53.0 3.98e-01 100.0% 33.3%
4994780 2484.1.1.124 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.69 60.0 4.13e-01 100.0% 29.8%
3621340 2002.1.1.30 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.67 50.0 3.61e-01 80.0% 28.8%
3474463 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.67 47.0 3.80e-01 75.0% 60.0%
5040091 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.66 55.0 3.56e-01 100.0% 18.7%
3928227 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.66 54.0 4.44e-01 100.0% 50.0%
3801037 7502.1.1.1 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 › HGTP_anticodon 0.65 51.0 3.85e-01 85.0% 40.0%
3408886 2004.1.1.30 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.64 52.0 3.12e-01 90.0% 19.6%
3343380 2002.1.1.19 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_17 0.64 47.0 3.22e-01 80.0% 55.1%
4976965 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.64 45.0 3.81e-01 85.0% 42.9%
4996735 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 54.0 3.94e-01 100.0% 32.8%
3405383 2005.1.1.36 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.63 48.0 3.38e-01 100.0% 24.2%
3524397 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.63 49.0 3.45e-01 100.0% 25.2%
4998772 2484.1.1.337 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RRXRR 0.63 50.0 3.91e-01 100.0% 36.4%
4886896 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.63 53.0 4.25e-01 96.7% 47.1%
5011606 2484.1.1.124 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.62 54.0 3.86e-01 100.0% 32.8%
3447478 2487.1.1.1 a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › Cpn60_TCP1 0.62 48.0 3.59e-01 83.3% 32.9%
3644199 2485.1.1.137 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DAHP_synth_2 0.62 47.0 3.91e-01 81.7% 47.6%
3643855 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.61 41.0 3.73e-01 80.0% 51.2%
3946483 2004.1.1.107 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DnaB_C 0.61 49.0 3.20e-01 100.0% 19.3%
4937514 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.61 52.0 4.01e-01 100.0% 48.0%
4246647 2003.1.1.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.61 46.0 3.62e-01 100.0% 38.5%
3697111 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.60 44.0 3.49e-01 85.0% 36.7%
1406486 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.60 52.0 4.11e-01 100.0% 60.6%
4358674 7503.1.1.3 a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › TolB_N 0.59 44.0 3.69e-01 83.3% 46.4%
5042296 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.58 48.0 3.88e-01 100.0% 46.3%
3954133 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.58 48.0 3.79e-01 100.0% 50.3%
4492083 309.1.2.3 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA-Thr_ED 0.58 50.0 3.92e-01 100.0% 45.6%
3518537 2007.1.2.10 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_3 0.57 43.0 3.44e-01 100.0% 38.5%
3210389 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.57 47.0 2.85e-01 95.0% 23.1%
4561209 7510.1.1.0 a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like 0.56 48.0 3.79e-01 100.0% 45.9%
3905027 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.56 39.0 3.18e-01 75.0% 60.0%
3591208 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 46.0 3.20e-01 95.0% 48.6%
5083595 2011.1.1.8 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.55 48.0 3.05e-01 100.0% 69.7%
4956132 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 0.54 47.0 3.85e-01 100.0% 87.8%
3626626 2485.1.1.109 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › PF26957 0.54 37.0 2.92e-01 75.0% 48.7%
2581850 7503.1.1.0 a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.53 37.0 3.88e-01 100.0% 80.4%
3503497 311.1.1.2 a+b three layers › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Band_3_cyto 0.51 35.0 2.39e-01 71.7% 41.4%
3991847 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 41.0 3.03e-01 100.0% 70.5%
D2 medium residues 61-123
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.74 58.0 4.35e-01 96.8% 34.8%
4ep4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.70 58.0 4.28e-01 96.8% 34.9%
4cc9B00 1.20.5.4730 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.70 48.0 4.11e-01 71.4% 62.2%
4evxA00 1.10.1740.240 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.57 50.0 4.39e-01 100.0% 89.7%
2cqnA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.55 38.0 3.69e-01 88.9% 62.3%
2fh0A00 1.10.8.140 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › PDCD5, DNA-binding domain 0.55 37.0 3.45e-01 81.0% 54.3%
3c1dA03 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 31.0 3.55e-01 73.0% 78.3%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.53 37.0 3.55e-01 74.6% 98.6%
2gxaE01 1.10.10.510 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Zinc finger, large T-antigen D1 domain 0.50 37.0 3.60e-01 88.9% 72.6%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4202129 2484.1.1.25 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.74 58.0 4.32e-01 96.8% 33.8%
4162427 2484.1.1.25 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.73 59.0 4.40e-01 95.2% 35.6%
4579381 2484.1.1.25 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.71 57.0 4.24e-01 96.8% 34.4%
2972075 3759.1.1.1 alpha arrays › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antiterm 0.57 46.0 4.45e-01 92.1% 91.5%
5002999 101.11.1.0 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.54 41.0 3.89e-01 90.5% 68.8%
3438472 219.1.1.23 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › MINDY_DUB 0.52 44.0 3.16e-01 100.0% 98.7%
4595954 101.11.1.0 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.52 42.0 3.92e-01 95.2% 78.8%
5073732 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 40.0 2.89e-01 95.2% 86.8%
4241236 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.50 40.0 3.77e-01 88.9% 71.2%