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SRR1747030_scaffold_3_prodigal-single.1__X__X__00016

Bact-Vir

SRR1747030_scaffold_3_prodigal-single.1__X__X__00016

Identity

Kingdom:
phage

Quality

88.6 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 4-58
PDB
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.77 68.0 5.43e-01 100.0% 62.0%
5mj3A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.73 59.0 5.11e-01 100.0% 57.5%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.73 56.0 3.46e-01 83.6% 53.3%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.71 61.0 4.39e-01 100.0% 94.0%
3nd1A02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.71 51.0 4.11e-01 78.2% 43.6%
2w01B00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.70 59.0 4.15e-01 100.0% 70.1%
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.70 57.0 5.32e-01 100.0% 72.2%
1m4jA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.69 61.0 4.61e-01 100.0% 47.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.69 60.0 5.11e-01 100.0% 95.7%
1y8qB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.67 52.0 3.50e-01 87.3% 60.8%
8hi1E01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 58.0 5.03e-01 100.0% 81.6%
3l2pA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.67 54.0 5.08e-01 100.0% 73.2%
7y8sB03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 57.0 5.01e-01 100.0% 67.9%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.66 50.0 5.14e-01 83.6% 96.0%
4ckbA01 3.30.470.140 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › 0.66 56.0 4.01e-01 100.0% 75.8%
6x3aA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 58.0 4.72e-01 100.0% 67.3%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.66 56.0 4.17e-01 100.0% 48.7%
4makB00 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 54.0 4.97e-01 100.0% 93.4%
1mw7A02 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.63 46.0 4.07e-01 87.3% 51.7%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 51.0 4.45e-01 89.1% 97.6%
2hpuA01 3.30.70.2060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 52.0 5.03e-01 98.2% 98.4%
2olsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.63 54.0 4.06e-01 100.0% 94.4%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 52.0 4.53e-01 100.0% 71.3%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.62 54.0 4.13e-01 100.0% 43.6%
5hv6A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.62 54.0 4.11e-01 100.0% 94.6%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.61 47.0 4.61e-01 100.0% 78.7%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 50.0 3.93e-01 100.0% 50.7%
2cs4A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.60 42.0 3.62e-01 81.8% 44.2%
1fp5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 51.0 4.25e-01 100.0% 63.0%
1k0rA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.58 36.0 3.04e-01 100.0% 34.3%
2gi3A01 3.90.1300.10 Alpha Beta › Alpha-Beta Complex › Amidase signature (AS) enzymes › Amidase signature (AS) domain 0.58 46.0 2.85e-01 94.5% 37.4%
1ud9A00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.57 46.0 3.06e-01 92.7% 47.5%
3jyuB01 3.30.2230.10 Alpha Beta › 2-Layer Sandwich › DUSP-like › DUSP-like 0.57 43.0 3.47e-01 89.1% 81.1%
2yweA03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.57 43.0 3.87e-01 85.5% 58.5%
6fezA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.56 47.0 4.08e-01 100.0% 61.7%
4ehoB03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.56 37.0 2.72e-01 70.9% 97.2%
2kvkA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 46.0 3.51e-01 100.0% 43.1%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 46.0 4.19e-01 100.0% 98.7%
3njaA02 2.10.70.100 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.54 38.0 4.14e-01 100.0% 89.1%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 41.0 3.78e-01 85.5% 80.3%
1ul7A00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.52 42.0 3.49e-01 90.9% 66.7%
4q0jA03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.52 41.0 3.21e-01 94.5% 51.4%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.52 40.0 3.12e-01 94.5% 48.4%
1g6q102 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.51 41.0 3.04e-01 100.0% 66.8%
2wadA02 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.51 36.0 2.82e-01 80.0% 30.4%
4perB00 3.10.130.10 Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain 0.51 38.0 3.19e-01 85.5% 68.8%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4399086 304.5.1.7 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.80 62.0 5.35e-01 83.6% 88.2%
4952123 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.77 69.0 6.75e-01 100.0% 95.0%
3691834 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.75 66.0 5.34e-01 100.0% 81.0%
5014007 3115.2.1.0 a+b two layers › GP2-like › GP2 › GP2 0.73 53.0 5.34e-01 78.2% 83.6%
5011497 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.72 63.0 4.30e-01 100.0% 72.5%
4961283 101.1.2.935 alpha arrays › HTH › HTH › winged helix domain › HVO_B0008_C 0.70 63.0 4.98e-01 100.0% 76.1%
3738773 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.68 55.0 5.52e-01 100.0% 90.9%
5036063 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.67 53.0 3.72e-01 89.1% 67.8%
5048876 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.67 57.0 5.47e-01 100.0% 92.3%
2098117 304.56.1.1 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › Cas_Cas2CT1978 0.66 56.0 4.79e-01 100.0% 75.8%
1106820 224.1.1.1 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.66 56.0 4.17e-01 100.0% 48.7%
4955641 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.66 46.0 3.83e-01 74.5% 99.0%
4309637 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.65 57.0 4.97e-01 100.0% 97.6%
3578252 101.21.1.1 alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › TP6A_N 0.65 44.0 3.50e-01 72.7% 35.0%
4974741 304.125.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in Api92-like proteins › ferredoxin-like domain in Api92-like proteins 0.65 54.0 4.80e-01 100.0% 97.6%
4889364 304.56.1.3 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › Cas3_I-F_Cas2 0.65 52.0 4.29e-01 100.0% 63.0%
4024040 822.1.1.0 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.64 54.0 5.23e-01 100.0% 87.7%
4935680 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 57.0 4.55e-01 100.0% 89.1%
3227231 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.64 49.0 4.74e-01 100.0% 74.6%
3611538 7.1.1.0 beta barrels › PDZ domain › PDZ domain › PDZ domain 0.64 47.0 4.75e-01 100.0% 83.6%
3970277 376.1.1.134 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › NosL 0.63 52.0 4.79e-01 98.2% 76.0%
3240033 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.63 45.0 2.87e-01 76.4% 60.6%
5075866 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.63 50.0 4.59e-01 94.5% 100.0%
3602264 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.63 44.0 3.88e-01 78.2% 48.2%
5013434 206.1.3.3 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › PPDK_N 0.63 49.0 3.26e-01 89.1% 62.4%
4989863 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.63 52.0 3.94e-01 96.4% 58.6%
5044372 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.62 54.0 4.31e-01 98.2% 88.2%
1915668 304.45.1.1 a+b two layers › Alpha-beta plaits › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › HPPK 0.62 51.0 3.60e-01 96.4% 58.3%
4394562 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.61 42.0 2.49e-01 70.9% 8.5%
3229807 822.1.1.0 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.61 52.0 4.71e-01 100.0% 68.8%
5001166 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.61 45.0 3.56e-01 85.5% 36.3%
3616815 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.61 42.0 4.18e-01 74.5% 86.7%
3695564 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 50.0 4.02e-01 94.5% 79.1%
3601845 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.61 51.0 3.46e-01 100.0% 26.5%
3244285 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.61 50.0 4.62e-01 100.0% 72.0%
3924928 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 50.0 4.20e-01 100.0% 64.8%
5055279 1075.1.2.0 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.60 48.0 3.33e-01 89.1% 91.7%
3723733 223.1.1.84 a+b three layers › Profilin-like › sensor domains › sensor domains › PHY+GAF 0.60 41.0 2.50e-01 72.7% 9.6%
None 0.60 41.0 2.46e-01 72.7% 8.7%
3321727 7.1.1.0 beta barrels › PDZ domain › PDZ domain › PDZ domain 0.59 47.0 4.49e-01 100.0% 75.7%
3831688 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.58 48.0 3.22e-01 96.4% 87.3%
4928686 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.56 40.0 3.56e-01 80.0% 61.1%
4950105 312.1.1.0 a+b three layers › HIT-like › HIT-related › HIT-related 0.56 47.0 3.40e-01 98.2% 45.1%
4977899 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 35.0 2.94e-01 70.9% 31.8%
3240741 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 43.0 2.64e-01 87.3% 39.1%
4680886 69.1.1.14 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hint_2 0.54 44.0 3.30e-01 100.0% 39.4%
5002173 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 38.0 3.25e-01 72.7% 43.3%
3719864 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 45.0 3.80e-01 100.0% 99.0%
5038375 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.54 41.0 2.90e-01 87.3% 35.5%
3907235 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.54 42.0 2.92e-01 94.5% 23.1%
3926827 101.1.2.394 alpha arrays › HTH › HTH › winged helix domain › eWH_GTF3C1 0.53 42.0 2.40e-01 87.3% 9.8%
3258276 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.53 43.0 2.97e-01 98.2% 23.6%
2029587 1146.1.1.1 few secondary structure elements › CRISPR-associated endonuclease C2c1 C-terminal domain › CRISPR-associated endonuclease C2c1 C-terminal domain › CRISPR-associated endonuclease C2c1 C-terminal domain › C2c1_Nuc-II 0.53 39.0 3.24e-01 85.5% 45.1%
3879988 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.52 39.0 2.69e-01 89.1% 21.4%
4330210 327.6.1.6 a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › Secretin 0.51 41.0 2.78e-01 100.0% 47.4%
4029830 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.51 38.0 2.90e-01 85.5% 41.3%