Back to structures

js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00159

Bact-Vir

js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00159

Identity

Kingdom:
phage

Quality

83.6 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 high residues 30-114
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ka2A00 1.10.1370.30 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › 0.71 57.0 3.48e-01 95.3% 14.7%
3hq2B00 1.10.1370.30 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › 0.70 57.0 3.51e-01 95.3% 15.1%
3hbvP01 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.67 52.0 4.44e-01 83.5% 71.0%
4l63A00 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.66 55.0 3.96e-01 91.8% 71.9%
5xdsA02 3.30.230.40 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › Imidazole glycerol phosphate dehydratase; domain 1 0.65 42.0 3.99e-01 96.5% 54.9%
6jebA01 3.30.379.10 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › Chitobiase/beta-hexosaminidase domain 2-like 0.65 42.0 4.44e-01 80.0% 74.7%
2qvpC00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.64 53.0 3.67e-01 88.2% 95.2%
2afcA00 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.63 48.0 3.99e-01 82.4% 75.2%
3p9dG02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.63 41.0 3.94e-01 80.0% 57.0%
2qcuB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.62 49.0 3.65e-01 87.1% 87.8%
4l4qB01 3.30.300.280 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › S-adenosylmethionine synthetase, C-terminal domain 0.62 44.0 3.68e-01 74.1% 93.1%
4okoA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.61 51.0 3.54e-01 91.8% 87.9%
3c4nA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.61 49.0 3.62e-01 88.2% 95.7%
6ks6G02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.61 41.0 3.82e-01 80.0% 55.8%
3nm6B00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.60 48.0 3.56e-01 87.1% 97.4%
3urrA00 3.40.930.10 Alpha Beta › 3-Layer(aba) Sandwich › Mannitol-specific EII; Chain A › Mannitol-specific EII; Chain A 0.60 47.0 3.95e-01 85.9% 53.9%
1y56B01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.60 46.0 3.45e-01 83.5% 85.7%
4paaA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.60 46.0 3.35e-01 83.5% 78.0%
3aq1B02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.59 40.0 3.72e-01 83.5% 53.6%
4g41A00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.59 48.0 3.52e-01 90.6% 95.3%
3if9A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 44.0 3.35e-01 83.5% 87.9%
4rslA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 44.0 3.31e-01 83.5% 86.7%
4wctA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 43.0 3.24e-01 83.5% 85.6%
2rghA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 48.0 3.43e-01 92.9% 81.5%
3gaaB00 3.40.50.10900 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PAC-like subunit 0.56 45.0 3.24e-01 85.9% 87.2%
3f4rA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 47.0 4.05e-01 94.1% 73.3%
4p02B04 3.30.379.30 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › 0.55 48.0 3.95e-01 97.6% 82.4%
3ozoA01 3.30.379.10 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › Chitobiase/beta-hexosaminidase domain 2-like 0.55 44.0 3.49e-01 88.2% 53.8%
4x9tA01 3.40.190.150 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Bordetella uptake gene, domain 1 0.55 38.0 3.12e-01 72.9% 51.5%
4cz2B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 44.0 3.51e-01 89.4% 89.4%
5iaiA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.54 47.0 3.61e-01 96.5% 53.1%
2gb3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 42.0 3.49e-01 85.9% 61.9%
5ar1A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 46.0 3.46e-01 96.5% 100.0%
1l9fA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 41.0 3.20e-01 84.7% 83.6%
4p02B02 3.30.379.20 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › 0.52 42.0 3.80e-01 90.6% 69.7%
7paxA01 3.40.1180.10 Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like 0.52 44.0 3.20e-01 97.6% 94.0%
1nowA01 3.30.379.10 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › Chitobiase/beta-hexosaminidase domain 2-like 0.51 43.0 3.77e-01 92.9% 62.8%
3k6kA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 41.0 2.83e-01 87.1% 85.9%
1p5hA01 3.40.50.10540 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Crotonobetainyl-coa:carnitine coa-transferase; domain 1 0.51 44.0 2.99e-01 95.3% 53.6%
6acsA00 3.40.1180.10 Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like 0.51 39.0 2.89e-01 83.5% 97.3%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4950654 2498.1.1.29 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M78 0.87 63.0 4.74e-01 83.5% 33.7%
5083216 2498.1.1.29 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M78 0.83 61.0 4.71e-01 89.4% 36.7%
4961836 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.77 64.0 5.39e-01 89.4% 55.0%
4961903 2498.1.1.29 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M78 0.77 63.0 5.30e-01 88.2% 53.6%
3717022 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.76 62.0 4.30e-01 87.1% 55.8%
3609379 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.75 62.0 5.43e-01 87.1% 81.7%
3704399 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.74 61.0 4.79e-01 87.1% 87.9%
3839854 2498.1.1.17 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YgjP-like 0.73 52.0 3.97e-01 85.9% 32.8%
3589463 2498.1.1.29 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M78 0.72 60.0 4.88e-01 89.4% 49.0%
3289507 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.71 56.0 4.72e-01 84.7% 51.4%
4937224 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.70 62.0 4.75e-01 95.3% 86.9%
5009806 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 51.0 3.87e-01 82.4% 87.3%
4112877 2498.1.1.122 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › PF29448 0.66 55.0 4.18e-01 90.6% 74.5%
3272315 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.65 56.0 4.45e-01 98.8% 51.7%
3731646 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.65 48.0 4.12e-01 80.0% 72.9%
3971289 2003.1.3.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.64 50.0 3.16e-01 83.5% 83.1%
None 0.63 50.0 3.23e-01 85.9% 88.0%
4681329 2003.1.2.12 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO 0.62 49.0 3.23e-01 87.1% 91.4%
4142761 2003.1.2.12 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO 0.62 52.0 3.79e-01 92.9% 85.4%
3803299 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.61 48.0 3.88e-01 83.5% 90.6%
2325720 2003.1.3.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.61 49.0 3.22e-01 87.1% 96.9%
3880429 2006.1.6.39 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › Mat89Bb 0.61 47.0 3.41e-01 83.5% 74.5%
4990159 2003.1.3.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.61 47.0 3.10e-01 83.5% 95.1%
4683120 2003.1.2.12 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO 0.61 51.0 3.77e-01 92.9% 85.8%
4037872 2003.1.3.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.61 49.0 3.54e-01 89.4% 92.5%
4936208 2484.1.1.137 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF2114 0.60 48.0 3.01e-01 87.1% 34.6%
4995119 2004.1.1.67 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CbiA 0.60 47.0 3.41e-01 83.5% 46.1%
3460106 244.1.1.4 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › DAO 0.60 41.0 3.09e-01 71.8% 79.1%
4667976 2004.1.2.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › PEP carboxykinase catalytic C-terminal domain 0.59 47.0 3.89e-01 87.1% 80.0%
4242144 2498.5.1.0 mixed a+b and a/b › Zincin-like › GroEL-intermediate domain like › GroEL-intermediate domain like 0.59 38.0 3.74e-01 76.5% 58.9%
4142165 2003.1.3.8 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › Mqo 0.59 46.0 3.21e-01 85.9% 81.6%
4051075 2498.2.1.2 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain › Glyco_hydro_67N 0.58 46.0 4.04e-01 85.9% 70.8%
4283884 7510.1.1.3 a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › FA_synthesis 0.58 48.0 3.93e-01 92.9% 88.8%
None 0.58 47.0 3.00e-01 89.4% 87.1%
3480695 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.58 43.0 3.29e-01 81.2% 48.8%
5042722 2004.1.1.175 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ParA 0.58 42.0 3.13e-01 78.8% 43.8%
4469293 2498.2.1.1 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain › Glyco_hydro_20b 0.58 47.0 4.05e-01 92.9% 60.7%
3814752 7534.1.1.1 a/b three-layered sandwiches › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase › Prenyltransf 0.57 42.0 3.09e-01 78.8% 33.9%
3414306 2498.2.1.4 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain › Glycohydro_20b2 0.56 44.0 3.44e-01 83.5% 54.4%
4598600 311.1.1.1 a+b three layers › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › PTS_EIIA_2 0.56 44.0 3.48e-01 84.7% 49.2%
4385967 327.17.1.2 a+b two layers › Alpha-lytic protease prodomain-like › S-adenosylmethionine synthetase › S-adenosylmethionine synthetase › AdoMet_Synthase 0.55 43.0 3.47e-01 83.5% 92.9%
3276582 2006.1.6.39 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › Mat89Bb 0.55 43.0 3.04e-01 83.5% 71.2%
4390756 311.1.1.1 a+b three layers › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › PTS_EIIA_2 0.55 42.0 3.45e-01 83.5% 54.5%
3640935 3543.1.1.4 alpha complex topology › Acid-activated urea channel › Acid-activated urea channel › Acid-activated urea channel › DUF716 0.55 49.0 3.58e-01 100.0% 49.4%
4236643 327.17.1.2 a+b two layers › Alpha-lytic protease prodomain-like › S-adenosylmethionine synthetase › S-adenosylmethionine synthetase › AdoMet_Synthase 0.55 38.0 3.34e-01 71.8% 93.1%
3397067 2498.2.1.4 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain › Glycohydro_20b2 0.55 44.0 3.50e-01 88.2% 52.2%
3327275 7579.1.1.51 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DUF676 0.54 40.0 2.61e-01 77.6% 19.8%
3439386 2004.1.1.26 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.53 38.0 2.59e-01 75.3% 65.6%
3932810 2498.5.1.0 mixed a+b and a/b › Zincin-like › GroEL-intermediate domain like › GroEL-intermediate domain like 0.53 40.0 3.55e-01 88.2% 54.4%
5079890 2004.1.1.570 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PF30762 0.53 40.0 3.06e-01 82.4% 51.4%
3174814 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.53 44.0 3.39e-01 98.8% 59.1%
3925246 2498.2.1.4 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain › Glycohydro_20b2 0.52 42.0 3.60e-01 89.4% 69.0%
3704361 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.52 39.0 2.60e-01 80.0% 72.4%
3864706 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 43.0 2.70e-01 96.5% 66.7%
3703337 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.51 36.0 2.54e-01 75.3% 32.7%