Back to structures

SRR1747065_scaffold_9_prodigal-single.1__X__X__00239

Bact-Vir

SRR1747065_scaffold_9_prodigal-single.1__X__X__00239

Identity

Kingdom:
phage

Quality

95.1 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 2-114
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00929.32 best RNase_T 42.6 1.30e-10 98.2% 67.1%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1j54A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.89 85.0 7.17e-01 100.0% 70.7%
2qxfA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.89 84.0 6.87e-01 100.0% 66.1%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.86 82.0 7.55e-01 100.0% 81.9%
4fzxC00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.85 70.0 6.10e-01 99.1% 59.4%
7t2sA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.83 78.0 6.61e-01 100.0% 69.1%
3mwpB02 3.30.420.410 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Arenaviral nucleoprotein, C-terminal domain 0.81 67.0 5.71e-01 99.1% 57.2%
2xriA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.77 71.0 5.74e-01 100.0% 62.9%
4qozB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.75 68.0 5.43e-01 100.0% 59.9%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.60 42.0 4.27e-01 100.0% 71.9%
2h3gX01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 41.0 4.53e-01 100.0% 98.9%
3djcB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 40.0 4.43e-01 100.0% 98.9%
3cqyA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 47.0 4.04e-01 100.0% 87.0%
1uwkA02 3.40.50.10730 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Urocanase like domains 0.52 39.0 3.18e-01 100.0% 42.3%
1toaA02 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.52 37.0 3.56e-01 100.0% 64.1%
2yx6D01 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.51 37.0 3.90e-01 100.0% 86.3%
3mcpA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 45.0 3.57e-01 100.0% 78.4%
7d73E01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.51 34.0 2.80e-01 100.0% 36.4%
1u6zA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.50 45.0 3.89e-01 100.0% 86.6%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5016375 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.98 96.0 7.71e-01 100.0% 60.0%
3963965 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.92 88.0 7.40e-01 100.0% 68.6%
4033087 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.90 86.0 6.68e-01 100.0% 51.4%
3945113 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.90 86.0 7.16e-01 100.0% 65.6%
4586442 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.90 86.0 6.67e-01 100.0% 51.8%
3953516 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.89 84.0 6.82e-01 100.0% 57.4%
3957139 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.89 84.0 6.75e-01 100.0% 56.0%
3988496 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.89 83.0 6.52e-01 100.0% 51.6%
5007230 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.89 85.0 6.85e-01 100.0% 57.9%
4103309 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.89 84.0 6.65e-01 100.0% 53.8%
3587075 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.88 83.0 7.10e-01 100.0% 65.9%
3280151 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.88 84.0 6.92e-01 100.0% 61.1%
3839669 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.88 83.0 6.17e-01 100.0% 43.5%
5062283 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.88 84.0 6.67e-01 100.0% 58.3%
3272730 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.87 83.0 6.75e-01 100.0% 59.1%
3088601 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.87 83.0 7.02e-01 100.0% 65.7%
4640906 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.87 83.0 6.71e-01 100.0% 57.9%
4031781 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.86 80.0 6.75e-01 100.0% 62.2%
4432985 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.86 81.0 6.54e-01 100.0% 57.0%
3971372 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.86 81.0 6.60e-01 100.0% 59.0%
4037317 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 81.0 6.46e-01 100.0% 55.1%
4176714 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 80.0 6.44e-01 100.0% 56.9%
4034216 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 80.0 6.55e-01 100.0% 57.9%
4052322 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 80.0 6.59e-01 100.0% 59.5%
3502270 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 71.0 6.07e-01 100.0% 58.2%
5024550 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 79.0 6.64e-01 99.1% 65.6%
4298195 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 80.0 6.45e-01 100.0% 56.5%
3822649 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 79.0 6.27e-01 100.0% 57.9%
2888739 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.83 78.0 6.58e-01 100.0% 68.4%
5081840 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.83 77.0 6.19e-01 100.0% 56.2%
4216340 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.83 77.0 6.35e-01 100.0% 63.7%
5081301 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.82 76.0 5.12e-01 100.0% 30.0%
4102293 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.81 76.0 6.24e-01 100.0% 61.1%
4931271 2484.1.1.68 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.80 62.0 4.98e-01 100.0% 43.8%
3988431 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.79 71.0 6.02e-01 100.0% 60.6%
4951831 2484.1.1.68 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.79 62.0 4.44e-01 100.0% 30.5%
3549895 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.75 69.0 5.46e-01 100.0% 58.7%
3378450 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.74 68.0 5.34e-01 100.0% 56.5%
5017856 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.68 62.0 4.69e-01 100.0% 57.4%
4224746 2484.1.1.37 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.64 42.0 4.25e-01 100.0% 67.3%
3662984 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 34.0 3.82e-01 98.2% 69.4%
3315568 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.60 37.0 4.61e-01 78.8% 100.0%
4438376 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.60 44.0 4.33e-01 99.1% 71.7%
3706725 2484.1.1.109 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › bVLRF1 0.58 52.0 4.51e-01 100.0% 72.2%
3512065 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 28.0 3.63e-01 70.8% 80.0%
5036237 2484.4.1.1 mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co 0.56 42.0 4.20e-01 100.0% 78.3%
4937776 2484.1.1.339 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › acVLRF1 0.55 40.0 4.19e-01 100.0% 82.9%
5024556 2484.4.1.1 mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co 0.54 43.0 4.41e-01 100.0% 90.9%
4010765 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.54 43.0 4.17e-01 100.0% 76.8%
4505130 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.54 46.0 4.45e-01 100.0% 82.4%
4985805 2484.4.1.1 mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co 0.54 41.0 4.12e-01 100.0% 80.0%
3597025 292.2.1.0 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.54 31.0 3.19e-01 100.0% 57.1%
5064572 2484.1.1.4 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.54 47.0 4.54e-01 100.0% 83.1%
5035771 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.54 48.0 4.58e-01 100.0% 83.8%
5079226 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.53 48.0 3.96e-01 100.0% 57.6%
4564292 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.53 41.0 4.10e-01 100.0% 80.0%
5054600 2484.1.1.10 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.53 42.0 4.21e-01 99.1% 83.5%
4984037 2484.4.1.1 mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co 0.53 40.0 3.72e-01 100.0% 63.4%
4955067 2484.4.1.1 mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co 0.52 40.0 4.05e-01 100.0% 83.6%
3220231 7517.1.1.1 a/b three-layered sandwiches › Nucleoside hydrolase › Nucleoside hydrolase › Nucleoside hydrolase › IU_nuc_hydro 0.50 44.0 3.18e-01 100.0% 72.9%
D2 high residues 116-199
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4j05A00 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.60 43.0 2.73e-01 75.0% 24.9%
2af6A02 6.10.140.450 Special › Helix non-globular › Helix Hairpins › 0.58 30.0 3.42e-01 73.8% 66.1%
7pbkA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 47.0 3.40e-01 90.5% 43.2%
4p63D00 3.40.910.10 Alpha Beta › 3-Layer(aba) Sandwich › Deoxyhypusine Synthase › Deoxyhypusine synthase 0.55 41.0 2.82e-01 79.8% 36.2%
3umbA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.53 35.0 3.65e-01 85.7% 72.2%
5hn3A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.50 43.0 2.92e-01 96.4% 92.8%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5016375 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.92 76.0 5.59e-01 89.3% 37.9%
3938610 180.1.1.1 alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2 0.59 43.0 3.14e-01 75.0% 85.0%
5012972 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.59 47.0 3.34e-01 85.7% 83.9%
3624159 193.1.1.26 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › CCDC22_N 0.56 44.0 3.97e-01 90.5% 96.0%
3400121 193.1.1.8 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › HOOK_N 0.56 46.0 3.81e-01 91.7% 74.8%
4028059 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.55 35.0 4.08e-01 96.4% 96.4%
3589919 102.1.4.2 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › Nop C-terminal domain › Transposase_20 0.53 46.0 3.89e-01 95.2% 70.0%