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SRR1747022_scaffold_43_prodigal-single.1__X__X__00005

Bact-Vir

SRR1747022_scaffold_43_prodigal-single.1__X__X__00005

Identity

Kingdom:
phage

Quality

77.1 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 5-89
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4i8oA02 3.30.160.690 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Bacterial toxin RNase RnlA/LsoA, N repeated domain 0.72 51.0 5.06e-01 89.4% 70.0%
3e5dA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.66 44.0 3.89e-01 91.8% 46.4%
4huzA02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.65 42.0 3.54e-01 91.8% 37.1%
1vjhA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.64 49.0 4.41e-01 90.6% 58.3%
4e6fA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.64 53.0 4.23e-01 90.6% 48.0%
2yweA05 3.30.70.2570 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation factor 4, C-terminal domain 0.64 41.0 4.47e-01 96.5% 80.9%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.63 45.0 4.64e-01 97.6% 78.0%
1w23A02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.62 46.0 4.32e-01 77.6% 74.8%
1cjxA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.62 39.0 3.23e-01 90.6% 35.3%
4xq7A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.62 51.0 4.20e-01 90.6% 77.6%
1q7lA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.61 47.0 3.67e-01 83.5% 68.2%
4jhyA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.61 50.0 4.12e-01 89.4% 48.7%
2vneA01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.61 50.0 4.07e-01 90.6% 64.4%
3jwhA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 42.0 3.28e-01 72.9% 96.3%
2h2yA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.60 40.0 3.68e-01 100.0% 50.9%
1nw1A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 44.0 4.29e-01 78.8% 94.8%
1a9xA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.58 33.0 3.58e-01 100.0% 65.7%
3kolA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.58 40.0 3.50e-01 90.6% 47.0%
5e4bA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.58 47.0 3.79e-01 91.8% 67.6%
2qqzA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.57 37.0 3.44e-01 90.6% 48.7%
3cueB00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.57 46.0 3.80e-01 91.8% 77.2%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 50.0 4.00e-01 98.8% 68.6%
1i1iP02 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.56 39.0 3.28e-01 74.1% 41.1%
2v7sA00 3.30.2030.20 Alpha Beta › 2-Layer Sandwich › TBP-like › 0.56 50.0 4.04e-01 100.0% 79.9%
2laeA00 3.30.310.170 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Outer membrane protein assembly factor BamC 0.56 44.0 3.96e-01 85.9% 61.0%
3tf8B00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.56 45.0 3.59e-01 90.6% 65.2%
1uyjA01 3.30.360.60 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › 0.56 41.0 4.21e-01 77.6% 97.6%
3cxbA01 3.30.2440.10 Alpha Beta › 2-Layer Sandwich › Secreted effector protein SifA fold › Secreted effector protein SifA 0.55 46.0 4.19e-01 91.8% 91.3%
1bywA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 40.0 3.75e-01 78.8% 93.6%
3bc8A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 49.0 4.19e-01 100.0% 79.0%
1uu1B01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 45.0 3.89e-01 89.4% 71.8%
3cloC01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 39.0 3.05e-01 75.3% 51.3%
6fyqA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 48.0 3.79e-01 97.6% 66.5%
2f7vA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 42.0 3.06e-01 84.7% 86.9%
4mjgA00 3.30.2030.30 Alpha Beta › 2-Layer Sandwich › TBP-like › 0.54 46.0 3.65e-01 94.1% 70.1%
4jpdA00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.54 40.0 3.69e-01 77.6% 67.0%
2bv4A00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.54 47.0 4.35e-01 100.0% 90.3%
1p97A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 38.0 3.48e-01 76.5% 81.6%
1mo7A00 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.53 42.0 3.20e-01 88.2% 45.1%
1k4nA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 44.0 3.55e-01 96.5% 73.8%
7jiuA03 3.30.1010.10 Alpha Beta › 2-Layer Sandwich › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 0.52 41.0 3.58e-01 88.2% 75.7%
5xogK00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.52 42.0 3.88e-01 90.6% 70.8%
3zi1A02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 42.0 3.57e-01 90.6% 86.9%
2jgtA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 44.0 3.79e-01 96.5% 75.9%
3ix3A00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.51 39.0 3.26e-01 84.7% 100.0%
1ykdB02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 40.0 3.24e-01 89.4% 97.9%
3ir3A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.51 41.0 3.67e-01 90.6% 81.7%
4e6nB00 3.30.1610.20 Alpha Beta › 2-Layer Sandwich › c-terminal autoproteolytic domain of nucleoporin nup98 › Hen1, N-terminal domain 0.50 35.0 2.74e-01 74.1% 76.1%
4rmmA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.50 40.0 3.48e-01 88.2% 63.0%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5073891 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.70 49.0 4.68e-01 89.4% 62.0%
5048999 331.9.1.0 ↗ a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.67 50.0 4.24e-01 90.6% 47.9%
4355722 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.67 47.0 4.52e-01 76.5% 64.2%
4346250 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.65 47.0 3.94e-01 75.3% 46.4%
4963533 2008.1.1.16 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.64 41.0 3.65e-01 78.8% 45.8%
3378755 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.63 46.0 4.06e-01 77.6% 52.0%
3213638 216.1.1.1 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UQ_con 0.62 46.0 3.82e-01 100.0% 43.9%
4977467 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.62 47.0 4.42e-01 100.0% 66.7%
5721 211.1.1.2 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › YecM 0.61 44.0 4.08e-01 91.8% 59.6%
3742793 601.23.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.61 44.0 3.04e-01 77.6% 26.6%
3719364 601.23.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.60 44.0 2.95e-01 76.5% 24.9%
4083689 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.60 48.0 4.50e-01 89.4% 87.2%
3979092 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.59 47.0 4.36e-01 90.6% 87.8%
3608730 601.23.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.59 42.0 2.87e-01 76.5% 24.9%
3446094 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.58 45.0 2.86e-01 84.7% 22.2%
5076160 284.1.2.0 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases 0.58 42.0 3.90e-01 98.8% 58.8%
4924545 206.1.3.10 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › CPSase_L_D2 0.58 35.0 3.00e-01 100.0% 35.4%
3537229 310.3.1.21 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › HNOB 0.58 40.0 3.81e-01 74.1% 93.3%
3270020 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.57 39.0 3.45e-01 78.8% 46.9%
3936241 216.1.1.1 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UQ_con 0.57 41.0 3.31e-01 100.0% 38.2%
3465399 331.3.1.43 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PDF2_C 0.56 46.0 3.43e-01 92.9% 72.1%
3929799 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.56 44.0 4.62e-01 92.9% 97.3%
3168846 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.55 39.0 3.65e-01 78.8% 58.2%
4942580 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.55 44.0 4.41e-01 98.8% 85.9%
3190430 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 47.0 3.68e-01 95.3% 47.6%
4028149 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.55 41.0 4.02e-01 90.6% 71.6%
2330628 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.54 44.0 3.48e-01 90.6% 63.2%
3267451 206.1.1.10 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Choline_kinase 0.54 41.0 2.76e-01 81.2% 22.2%
3492823 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.54 43.0 3.44e-01 90.6% 62.6%
4931358 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.54 39.0 3.51e-01 76.5% 80.8%
3484278 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.54 44.0 3.47e-01 92.9% 48.2%
3966115 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 37.0 3.05e-01 71.8% 76.9%
4992091 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.53 42.0 2.68e-01 88.2% 25.6%
3760913 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.53 42.0 3.84e-01 91.8% 97.6%
3217507 243.1.1.98 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF5382_C 0.52 39.0 3.66e-01 96.5% 62.3%
4034422 3425.2.1.3 ↗ a+b three layers › Two-component system yycF/yycG regulatory protein yycH-like › YycH C-terminal domain › YycH C-terminal domain › PF29809 0.52 41.0 3.07e-01 89.4% 33.9%
3405822 220.1.1.43 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SIN1_PH 0.52 44.0 3.70e-01 92.9% 57.9%
4029264 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 45.0 3.82e-01 97.6% 64.3%
4973090 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.51 36.0 3.44e-01 74.1% 74.0%
3993688 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.51 45.0 3.76e-01 97.6% 79.3%
4973597 3016.1.1.4 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Pyridoxal_deC 0.51 44.0 3.89e-01 98.8% 71.5%
4096825 331.3.1.8 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Lipoprotein_18 0.51 44.0 3.98e-01 96.5% 71.3%
1177460 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.50 37.0 3.38e-01 78.8% 78.0%
3735309 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 37.0 3.69e-01 78.8% 86.7%