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BML_08182015_6_5m_scaffold_7_prodigal-single.1__X__X__00234

Bact-Vir

BML_08182015_6_5m_scaffold_7_prodigal-single.1__X__X__00234

Identity

Kingdom:
phage

Quality

67.8 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 3-61
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o5iN05 1.10.40.90 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › 0.68 50.0 5.27e-01 84.7% 90.4%
3fghA00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.67 57.0 5.56e-01 98.3% 91.0%
1uyvB02 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.67 46.0 2.90e-01 71.2% 19.9%
1ztdA00 1.10.1520.20 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III 0.63 54.0 4.33e-01 100.0% 89.6%
1wtyA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.58 41.0 3.35e-01 98.3% 38.8%
1sfxB00 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 43.0 3.55e-01 100.0% 46.2%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.57 36.0 3.37e-01 100.0% 51.4%
2ga8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 44.0 2.73e-01 88.1% 30.4%
5svlA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.54 42.0 4.04e-01 98.3% 75.0%
3nivC02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 39.0 3.19e-01 100.0% 39.5%
6k4yI00 1.10.1810.10 Mainly Alpha › Orthogonal Bundle › Anti-sigma factor AsiA › Anti-Sigma Factor A 0.52 39.0 3.56e-01 86.4% 86.4%
2n80A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.52 37.0 3.32e-01 79.7% 100.0%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4073169 4951.1.1.0 alpha arrays › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit 0.80 52.0 6.11e-01 72.9% 100.0%
4977712 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.75 66.0 3.77e-01 93.2% 12.3%
4943371 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.70 44.0 4.23e-01 84.7% 54.3%
4018335 141.1.1.3 alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › UbiA 0.57 47.0 3.04e-01 98.3% 60.0%
4988587 102.1.2.18 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › OGG_N 0.57 42.0 2.79e-01 79.7% 57.0%
4020710 3924.1.1.1 alpha complex topology › Sterol uptake control protein 2 › Sterol uptake control protein 2 › Sterol uptake control protein 2 › Fungal_trans_2 0.57 44.0 2.73e-01 89.8% 16.5%
3866056 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.55 47.0 2.83e-01 100.0% 69.0%
4049765 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.55 47.0 2.80e-01 100.0% 30.3%
3289222 141.1.1.3 alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › UbiA 0.54 47.0 3.02e-01 100.0% 41.6%
3444202 4267.1.1.4 a+b duplicates or obligate multimers › YefM-like › YefM-like › YefM-like › p450 0.54 45.0 3.00e-01 94.9% 65.1%
3651312 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.53 46.0 2.74e-01 100.0% 31.5%
None 0.52 41.0 2.91e-01 91.5% 50.5%
D2 medium residues 99-137
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ga8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.85 64.0 3.68e-01 82.1% 11.2%
4muoA02 3.40.1030.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 0.84 61.0 3.67e-01 76.9% 12.6%
3c5vA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.76 58.0 3.46e-01 87.2% 69.0%
3qitB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.75 62.0 3.69e-01 92.3% 15.2%
3hz6A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.73 51.0 3.10e-01 74.4% 11.7%
1wj7A01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.72 54.0 4.79e-01 87.2% 55.0%
1xf1A01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.72 60.0 3.54e-01 97.4% 19.0%
4ixjA01 3.30.1300.80 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.70 52.0 4.28e-01 84.6% 48.1%
7dklA02 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 0.70 55.0 4.33e-01 92.3% 58.9%
3clqA03 1.10.10.660 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › conserved protein of unknown function from Enterococcus faecalis V583 0.68 57.0 4.82e-01 100.0% 55.7%
1bi0A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.68 53.0 4.73e-01 100.0% 65.2%
1wgfA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.67 53.0 4.98e-01 100.0% 90.6%
2ekfA01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.66 48.0 4.65e-01 87.2% 69.6%
1uyvB02 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.65 50.0 3.05e-01 94.9% 18.6%
1nrwA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.64 53.0 3.79e-01 100.0% 43.8%
1kl7A02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 51.0 3.16e-01 100.0% 21.2%
4g6dB02 6.10.140.1800 Special › Helix non-globular › Helix Hairpins › 0.61 43.0 3.56e-01 79.5% 61.7%
2e1qC10 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.61 51.0 3.58e-01 97.4% 37.5%
5eowA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 49.0 2.88e-01 100.0% 96.0%
3jsjC00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 38.0 2.57e-01 79.5% 15.3%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.53 41.0 3.01e-01 100.0% 30.1%
2uytA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 38.0 2.44e-01 89.7% 31.6%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3741429 2004.1.1.44 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PRK 0.89 67.0 4.09e-01 82.1% 15.9%
5022566 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.88 65.0 5.77e-01 79.5% 56.4%
3980440 7544.1.1.0 a/b three-layered sandwiches › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 0.86 62.0 3.67e-01 76.9% 11.8%
3283939 3781.2.1.0 a+b two layers › Ribosomal protein L11/L12e N-terminal domain-like › ssDNA-binding protein ThermoDBP-related › ssDNA-binding protein ThermoDBP-related 0.82 64.0 4.33e-01 87.2% 45.5%
4526271 7544.1.1.1 a/b three-layered sandwiches › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain › Glycos_transf_3 0.82 68.0 4.05e-01 92.3% 15.4%
4977712 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.80 68.0 3.80e-01 100.0% 8.0%
3165338 2484.1.1.32 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_C 0.80 55.0 3.37e-01 71.8% 13.0%
4142281 105.1.1.55 alpha duplicates or obligate multimers › HLH-like › HLH, helix-loop-helix DNA-binding domain › HLH, helix-loop-helix DNA-binding domain › Latarcin 0.80 68.0 5.18e-01 100.0% 44.7%
4061431 190.1.1.0 alpha arrays › HMG-box-like › HMG-box › HMG-box 0.77 63.0 5.78e-01 89.7% 82.0%
4139843 275.1.1.0 a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.76 63.0 6.03e-01 94.9% 100.0%
4263695 4951.1.1.0 alpha arrays › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit › inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit 0.75 62.0 6.19e-01 94.9% 97.5%
3966250 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.74 61.0 6.15e-01 97.4% 100.0%
3165406 4959.1.1.0 a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit 0.73 60.0 6.00e-01 94.9% 97.5%
3590235 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.73 61.0 3.99e-01 100.0% 23.9%
3407104 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.70 54.0 4.32e-01 89.7% 64.7%
3503648 190.1.1.1 alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.68 59.0 5.16e-01 100.0% 76.7%
D3 medium residues 141-189
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5mz2I00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.65 53.0 4.00e-01 100.0% 37.4%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.65 50.0 5.01e-01 100.0% 88.0%
3tupA02 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.63 50.0 4.16e-01 93.9% 90.6%
3b49A00 3.20.80.10 Alpha Beta › Alpha-Beta Barrel › Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A › Regulatory factor, effector binding domain 0.62 52.0 3.52e-01 100.0% 52.5%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.62 51.0 4.41e-01 100.0% 90.6%
1auvA01 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.62 45.0 4.35e-01 100.0% 68.3%
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.61 50.0 4.11e-01 100.0% 84.3%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 50.0 3.55e-01 100.0% 44.3%
3e7wA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.59 44.0 3.55e-01 85.7% 73.0%
3cp2A02 2.40.30.260 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.58 46.0 3.86e-01 98.0% 100.0%
2z5bB01 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.57 40.0 3.06e-01 81.6% 31.1%
1a9xA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.55 41.0 3.78e-01 100.0% 61.4%
7whgG02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 46.0 3.83e-01 100.0% 51.1%
2ldyA01 3.30.70.1820 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › L1 transposable element, RRM domain 0.55 43.0 3.65e-01 98.0% 99.0%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.55 44.0 3.99e-01 100.0% 100.0%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.54 42.0 4.07e-01 100.0% 75.0%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 44.0 3.69e-01 98.0% 91.5%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 44.0 3.96e-01 100.0% 68.4%
6pl6B01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 43.0 2.71e-01 100.0% 62.4%
3b7kB01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.53 41.0 3.00e-01 85.7% 69.3%
1ii5A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 43.0 3.20e-01 95.9% 46.9%
3flkA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.51 42.0 2.60e-01 98.0% 31.5%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3300115 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.64 55.0 4.38e-01 100.0% 52.4%
3838763 304.44.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.64 54.0 4.58e-01 98.0% 100.0%
4945426 206.1.3.2 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › GARS_A 0.63 50.0 3.28e-01 89.8% 37.0%
5030867 304.160.1.1 a+b two layers › Alpha-beta plaits › Gas vesicle protein GvpF › Gas vesicle protein GvpF › GvpL_GvpF 0.62 53.0 4.26e-01 100.0% 81.0%
3582833 221.1.1.6 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.62 49.0 3.94e-01 100.0% 41.8%
3719882 148.1.3.45 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DYN_lid 0.59 47.0 3.19e-01 85.7% 52.7%
5016503 77.1.1.0 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein 0.59 49.0 3.92e-01 100.0% 50.9%
5080205 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.58 43.0 4.29e-01 100.0% 88.0%
3783088 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 46.0 4.19e-01 100.0% 97.3%
5013194 3115.4.1.0 a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 0.57 45.0 4.49e-01 100.0% 94.5%
3264069 822.1.1.2 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF_2 0.56 43.0 4.12e-01 100.0% 75.0%
4165803 206.1.3.11 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › GSH-S_ATP 0.54 41.0 2.89e-01 100.0% 22.6%
3197560 301.6.1.0 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like 0.53 40.0 2.66e-01 81.6% 38.5%
3434909 221.1.1.166 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PF26130 0.51 36.0 3.38e-01 100.0% 57.1%