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PH2015_20_scaffold_1_prodigal-single.1__X__X__00353

Bact-Vir

PH2015_20_scaffold_1_prodigal-single.1__X__X__00353

Identity

Kingdom:
phage

Quality

75.7 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 23-120
PDB
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4euyA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.69 51.0 5.36e-01 86.7% 88.4%
1t4yA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.68 54.0 5.61e-01 83.7% 100.0%
3pqvA02 3.30.360.20 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › RNA 3'-terminal phosphate cyclase, insert domain 0.67 53.0 5.36e-01 85.7% 92.7%
3ly7A01 3.40.50.11830 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.67 53.0 4.55e-01 86.7% 72.7%
2dm9A00 3.30.2320.30 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › ATP synthase, E subunit, C-terminal 0.66 40.0 3.74e-01 70.4% 49.2%
2diyA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.66 55.0 5.25e-01 89.8% 78.4%
5gu6A02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.65 51.0 5.12e-01 89.8% 82.2%
4f9zA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.65 51.0 5.09e-01 85.7% 80.6%
6izhE00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.65 38.0 3.55e-01 90.8% 46.3%
7p8na01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.64 45.0 4.85e-01 81.6% 86.7%
4o89A02 3.30.360.20 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › RNA 3'-terminal phosphate cyclase, insert domain 0.63 51.0 5.25e-01 89.8% 93.6%
3kgkB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.63 49.0 4.93e-01 82.7% 88.8%
2hp0A02 3.30.1330.120 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 2-methylcitrate dehydratase PrpD 0.63 44.0 4.01e-01 72.4% 77.9%
2uzhA00 3.30.1330.50 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 0.62 40.0 3.43e-01 90.8% 41.2%
6k96B02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.61 42.0 4.24e-01 70.4% 76.3%
2yv9A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 48.0 4.60e-01 82.7% 80.9%
3lmeC00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.61 35.0 3.25e-01 86.7% 43.3%
2es7A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.60 47.0 4.64e-01 82.7% 80.6%
5vegB00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.60 49.0 4.23e-01 86.7% 99.3%
1iloA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.60 44.0 4.88e-01 82.7% 100.0%
1edzA02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.60 51.0 4.64e-01 92.9% 81.7%
4c6sA00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.59 49.0 4.36e-01 89.8% 99.3%
2ewcB00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.59 36.0 3.36e-01 90.8% 48.8%
3quwA00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.58 34.0 3.20e-01 89.8% 44.8%
3i7tA00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.57 34.0 3.22e-01 88.8% 47.5%
3euaA03 3.40.50.12570 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 39.0 4.00e-01 70.4% 90.4%
3v4dB00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.56 32.0 3.04e-01 88.8% 44.0%
3fj1A01 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.56 43.0 3.47e-01 82.7% 66.8%
2ig8A00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.55 34.0 3.09e-01 89.8% 42.3%
3lybC00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.55 33.0 3.03e-01 89.8% 42.5%
1dbfA00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.55 38.0 3.52e-01 71.4% 55.9%
2h3hA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 49.0 4.26e-01 100.0% 95.9%
2bonA01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.54 49.0 4.47e-01 100.0% 98.4%
5fc1A01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.54 46.0 3.15e-01 100.0% 90.5%
2h0aA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 48.0 4.60e-01 100.0% 94.6%
2qi2A03 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.53 32.0 3.34e-01 85.7% 62.8%
2qnkA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 46.0 3.37e-01 100.0% 42.7%
6gs2C01 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.52 42.0 3.27e-01 90.8% 88.0%
7yosA01 3.90.1640.30 Alpha Beta › Alpha-Beta Complex › inorganic pyrophosphatase (n-terminal core) › 0.52 39.0 3.14e-01 79.6% 65.4%
4hslA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 44.0 3.73e-01 94.9% 73.5%
1zvfB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 44.0 3.77e-01 96.9% 73.8%
3ir1B01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 40.0 3.61e-01 83.7% 75.6%
1xs5A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 40.0 3.61e-01 83.7% 77.6%
1otgA00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.51 42.0 3.95e-01 91.8% 88.8%
3up9A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 40.0 3.57e-01 83.7% 78.3%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3982265 298.4.1.0 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E 0.78 43.0 4.46e-01 70.4% 56.8%
3677519 2484.1.1.106 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF659 0.74 43.0 3.18e-01 90.8% 24.3%
4028204 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.74 55.0 6.00e-01 86.7% 95.0%
4943448 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.73 44.0 4.14e-01 90.8% 49.2%
5049605 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.73 39.0 4.99e-01 87.8% 92.7%
4026241 2485.2.1.0 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain 0.70 58.0 5.61e-01 90.8% 94.5%
5080313 2485.1.1.38 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_3 0.69 56.0 5.94e-01 91.8% 100.0%
4945290 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.69 38.0 4.73e-01 87.8% 88.3%
3300991 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.69 59.0 5.53e-01 94.9% 96.7%
3727816 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.69 54.0 5.46e-01 88.8% 83.0%
3881647 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.68 58.0 5.66e-01 94.9% 95.5%
4888978 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.68 57.0 5.61e-01 92.9% 91.5%
3828102 2485.1.1.56 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.67 54.0 4.38e-01 86.7% 64.7%
5041554 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.67 56.0 5.72e-01 91.8% 94.7%
3544989 2485.1.1.43 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_6 0.66 53.0 5.22e-01 85.7% 79.0%
4376550 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.66 53.0 5.38e-01 86.7% 97.9%
3585580 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.66 51.0 4.94e-01 82.7% 72.7%
3738850 2485.1.1.43 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_6 0.66 59.0 5.62e-01 99.0% 83.5%
3266908 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.66 52.0 5.21e-01 86.7% 98.0%
5082943 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.66 57.0 5.63e-01 96.9% 91.4%
3737843 2485.1.1.43 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_6 0.66 59.0 4.26e-01 99.0% 54.9%
3976963 7503.1.1.18 a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › PF30449 0.66 53.0 4.80e-01 86.7% 90.8%
4000097 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.65 48.0 4.58e-01 80.6% 67.0%
3500298 2485.1.1.87 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › UBX7_N 0.64 58.0 5.46e-01 100.0% 80.8%
5033745 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.64 49.0 5.07e-01 83.7% 87.2%
5058142 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.64 53.0 5.32e-01 92.9% 93.0%
3216096 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.63 52.0 4.91e-01 89.8% 75.0%
4942053 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.63 36.0 3.85e-01 84.7% 64.7%
3747082 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.63 49.0 4.92e-01 89.8% 82.0%
4583701 301.7.1.1 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › Ribonuc_L-PSP 0.62 36.0 3.38e-01 90.8% 44.0%
4155570 2485.1.1.43 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_6 0.62 47.0 4.76e-01 86.7% 79.0%
3237096 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.62 50.0 5.27e-01 85.7% 98.8%
4179560 301.5.1.1 a+b three layers › Bacillus chorismate mutase-like › 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF › 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF › YgbB 0.62 39.0 3.36e-01 90.8% 39.4%
2429757 301.7.1.1 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › Ribonuc_L-PSP 0.61 36.0 3.26e-01 91.8% 40.6%
None 0.61 37.0 2.91e-01 70.4% 28.3%
4137825 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.61 39.0 4.08e-01 96.9% 71.1%
4965641 301.7.1.1 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › Ribonuc_L-PSP 0.60 34.0 3.23e-01 88.8% 44.2%
3743243 245.1.1.1 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.60 30.0 3.23e-01 70.4% 55.3%
3972461 301.7.1.1 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › Ribonuc_L-PSP 0.60 35.0 3.23e-01 89.8% 42.3%
5083812 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.60 49.0 4.98e-01 87.8% 96.8%
3944872 7503.1.1.10 a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › CadC_C1 0.59 49.0 4.37e-01 90.8% 82.9%
3795869 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.59 51.0 4.40e-01 99.0% 60.0%
6994 301.7.1.0 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like 0.58 36.0 3.36e-01 90.8% 49.2%
4968882 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.57 36.0 4.30e-01 89.8% 96.9%
3260693 2004.1.1.19 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.57 46.0 3.95e-01 91.8% 86.5%
5042329 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.57 37.0 3.86e-01 88.8% 71.0%
3279529 301.7.1.1 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like › Ribonuc_L-PSP 0.56 33.0 3.09e-01 88.8% 44.0%
3938530 2484.1.1.66 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_3 0.56 44.0 3.33e-01 92.9% 36.4%
4536901 563.1.1.1 alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.54 36.0 3.02e-01 74.5% 38.8%
3730029 2007.1.3.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.52 44.0 3.44e-01 91.8% 93.3%
4011970 301.7.1.0 a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like 0.52 32.0 2.94e-01 89.8% 44.6%
3692938 10.12.1.30 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › 3-HAO 0.52 45.0 3.62e-01 94.9% 65.8%
4480600 2007.1.4.3 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain › NAD_kinase 0.52 46.0 4.50e-01 100.0% 99.1%
None 0.52 44.0 3.68e-01 94.9% 69.3%
None 0.51 44.0 3.67e-01 94.9% 70.1%
4608068 10.12.1.30 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › 3-HAO 0.50 44.0 3.60e-01 96.9% 64.1%
None 0.50 39.0 2.67e-01 83.7% 98.0%
3508543 7523.1.1.0 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.50 41.0 3.17e-01 86.7% 46.2%