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JGI24723J26617_10000007_prodigal-single.1__X__X__00221

Bact-Vir

JGI24723J26617_10000007_prodigal-single.1__X__X__00221

Identity

Kingdom:
phage

Quality

72.4 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 10-85
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cc1L00 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.67 47.0 2.88e-01 75.0% 97.5%
1ospO01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.65 41.0 3.73e-01 82.9% 46.7%
1i1iP02 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.64 46.0 3.69e-01 76.3% 82.8%
7pikC01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 46.0 3.43e-01 84.2% 82.6%
3zyyX04 3.30.420.480 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Domain of unknown function (DUF4445) 0.60 49.0 3.67e-01 89.5% 95.2%
3n4pC00 3.30.420.320 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › DNA-packaging terminase, C-terminal nuclease domain 0.59 48.0 3.58e-01 93.4% 86.7%
2i0rA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 49.0 3.20e-01 93.4% 43.3%
1vw4502 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 42.0 3.93e-01 75.0% 69.6%
1sz2B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 47.0 4.13e-01 92.1% 94.2%
5xd7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 42.0 3.61e-01 78.9% 89.8%
3stoA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.57 45.0 3.67e-01 85.5% 74.7%
2af5A02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.57 37.0 3.03e-01 82.9% 36.2%
2oztA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 42.0 3.71e-01 80.3% 98.3%
4g79A00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.57 44.0 3.72e-01 85.5% 95.5%
1nmnA00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.57 46.0 4.04e-01 90.8% 100.0%
2qe8A00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.57 47.0 3.12e-01 94.7% 51.0%
2l2mA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 39.0 4.03e-01 71.1% 88.6%
3ctkA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.56 46.0 3.64e-01 92.1% 99.4%
1vhxB00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.56 45.0 3.77e-01 90.8% 100.0%
2zshA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 39.0 2.61e-01 75.0% 27.8%
2asbA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 4.08e-01 77.6% 85.3%
2kzxA00 3.90.1010.20 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.55 45.0 3.84e-01 93.4% 92.4%
3da8B00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.55 42.0 3.15e-01 84.2% 53.2%
3cqzH00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 3.59e-01 80.3% 87.1%
2w35A00 3.30.2170.10 Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily 0.54 44.0 3.23e-01 92.1% 77.6%
4o8uA00 3.30.420.440 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF4152 0.54 42.0 3.15e-01 89.5% 83.7%
2gtlO02 2.40.128.620 Mainly Beta › Beta Barrel › Lipocalin › 0.54 48.0 3.76e-01 100.0% 71.2%
4ikbA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 37.0 3.15e-01 71.1% 89.9%
3o6uC00 3.90.1010.20 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.54 44.0 3.86e-01 93.4% 94.1%
3wx1A00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.53 36.0 3.29e-01 77.6% 50.0%
2xetB00 2.60.40.2070 Mainly Beta › Sandwich › Immunoglobulin-like › PapC, C-terminal domain 0.53 40.0 3.82e-01 78.9% 83.0%
1bcoA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 42.0 3.06e-01 86.8% 81.5%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.53 37.0 3.23e-01 96.1% 47.0%
1k8kD02 3.30.1460.20 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.53 37.0 3.18e-01 75.0% 65.6%
3gocA00 3.30.2170.10 Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily 0.53 44.0 3.17e-01 93.4% 77.2%
2re2A00 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.53 45.0 3.95e-01 97.4% 92.4%
1ojtA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.53 43.0 3.69e-01 89.5% 81.1%
2zadA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 38.0 3.44e-01 80.3% 95.6%
3gd6A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 40.0 3.43e-01 88.2% 95.8%
5amhA00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.52 35.0 3.24e-01 75.0% 50.9%
4ua3A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 36.0 2.80e-01 75.0% 74.2%
4kghA00 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.51 39.0 3.00e-01 84.2% 61.7%
2e5aA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.51 35.0 3.29e-01 71.1% 76.3%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 41.0 3.88e-01 93.4% 93.8%
1qy9A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 36.0 2.91e-01 76.3% 80.4%
2o7rA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 39.0 2.74e-01 89.5% 37.5%
2ychA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 43.0 3.45e-01 96.1% 98.1%
5aa5E00 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.50 41.0 2.49e-01 93.4% 96.4%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3617987 4099.1.1.28 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › PF29108 0.68 44.0 4.26e-01 88.2% 58.8%
3961733 330.10.1.0 a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain 0.68 47.0 4.50e-01 72.4% 66.7%
4877157 77.1.1.1 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1 0.67 42.0 2.79e-01 81.6% 15.5%
4386515 330.1.1.30 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF27148 0.65 44.0 4.73e-01 71.1% 95.4%
4606694 4099.1.1.26 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Kre28 0.62 43.0 4.24e-01 73.7% 81.9%
3429608 109.4.1.1256 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.62 43.0 2.46e-01 73.7% 7.1%
3600147 897.1.1.0 a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.62 53.0 3.85e-01 98.7% 74.8%
3922382 2484.1.1.242 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rva_4 0.61 46.0 3.36e-01 81.6% 71.1%
3914424 2484.1.1.242 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rva_4 0.61 47.0 3.34e-01 81.6% 67.4%
3718455 277.1.1.0 a+b two layers › PX domain › PX domain › PX domain 0.61 43.0 3.78e-01 73.7% 95.6%
5069904 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.60 43.0 3.56e-01 76.3% 80.0%
4029631 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.60 42.0 3.75e-01 72.4% 91.4%
4346434 2484.1.1.40 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.59 49.0 4.00e-01 89.5% 97.8%
4988847 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.59 43.0 4.41e-01 81.6% 80.0%
3412971 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.58 41.0 3.64e-01 73.7% 80.0%
5063704 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 43.0 4.60e-01 81.6% 92.3%
4334199 77.1.1.1 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1 0.57 39.0 3.33e-01 86.8% 43.2%
195810 5.1.3.11 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › MRJP 0.57 47.0 3.12e-01 94.7% 51.0%
3219786 11.2.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.56 42.0 3.51e-01 80.3% 69.6%
3376912 2484.1.1.165 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 42.0 2.71e-01 82.9% 96.9%
4527351 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 41.0 2.67e-01 80.3% 37.0%
3614206 213.1.1.31 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_10 0.56 39.0 2.73e-01 75.0% 70.4%
3669367 2484.1.1.165 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 42.0 2.80e-01 82.9% 95.8%
3363185 2484.1.1.106 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF659 0.55 43.0 2.89e-01 85.5% 97.2%
3938933 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 47.0 3.74e-01 93.4% 69.7%
3867030 2484.1.1.104 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_1 0.55 44.0 3.21e-01 92.1% 71.8%
3659523 11.2.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.55 41.0 3.57e-01 81.6% 76.0%
3687101 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 46.0 3.11e-01 94.7% 68.3%
4312891 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 42.0 3.23e-01 85.5% 81.6%
3656110 5.1.3.144 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.54 47.0 3.10e-01 97.4% 81.4%
3743052 5.1.4.78 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › TFIIIC_delta 0.54 45.0 2.91e-01 100.0% 82.9%
3704961 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.54 38.0 2.70e-01 75.0% 73.1%
3816742 5.1.3.118 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.54 44.0 2.97e-01 94.7% 79.7%
5075712 2484.1.1.55 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.54 41.0 3.21e-01 84.2% 79.4%
3955433 2484.1.1.9 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.54 41.0 3.22e-01 85.5% 83.3%
3563980 2484.1.1.104 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_1 0.53 42.0 2.98e-01 90.8% 72.9%
3462291 5.1.3.142 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_AT5G49610-like 0.53 46.0 3.13e-01 100.0% 82.6%
3588441 2484.1.1.194 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve, rve_3 0.53 41.0 3.28e-01 85.5% 87.3%
3678038 2.1.1.76 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › REPA_OB_2 0.53 38.0 3.85e-01 77.6% 98.7%
1883326 4998.2.1.1 beta sandwiches › Flagellar hook protein flgE D2 domain-like › Flagellar hook protein flgE insert domain › Flagellar hook protein flgE insert domain › FlgE_2nd 0.53 48.0 4.00e-01 100.0% 92.1%
5030209 244.3.1.0 a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU 0.53 41.0 3.47e-01 86.8% 94.1%
4265925 3518.1.2.0 a+b two layers › putative RnfG subunit of electron transport complex › putative RnfG subunit of electron transport complex 0.52 46.0 3.74e-01 100.0% 61.7%
4951890 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 41.0 3.66e-01 89.5% 95.7%
5003367 2484.1.1.23 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydantoinase_A 0.52 42.0 3.47e-01 93.4% 72.7%
3733585 2484.1.1.49 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydant_A_N 0.51 43.0 3.35e-01 94.7% 66.9%
3217505 9.1.1.55 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF7045 0.51 46.0 4.00e-01 100.0% 89.6%
4564833 2485.1.1.93 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like_DJC16_2nd 0.51 36.0 3.14e-01 75.0% 84.8%
5054991 5.1.11.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed 0.51 42.0 3.02e-01 90.8% 62.3%
3846927 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 35.0 3.36e-01 73.7% 61.1%