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SRR1747018_scaffold_13_prodigal-single.1__X__X__00025

Bact-Vir

SRR1747018_scaffold_13_prodigal-single.1__X__X__00025

Identity

Kingdom:
phage

Quality

78.7 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 165-219
PDB
CATH (58)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4lq0A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.76 67.0 4.93e-01 100.0% 47.6%
3hyiA01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.74 63.0 4.40e-01 100.0% 31.4%
1j4wA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.74 52.0 4.71e-01 74.5% 66.2%
3e54A00 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.73 64.0 4.60e-01 100.0% 43.4%
3pehA02 3.30.70.2140 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.72 50.0 5.38e-01 74.5% 90.9%
1nf2A02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.72 66.0 5.20e-01 100.0% 86.8%
3qwuA03 3.30.70.2160 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 49.0 3.69e-01 74.5% 34.5%
2fb0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 49.0 4.17e-01 74.5% 55.3%
2mzwA01 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.69 48.0 4.39e-01 74.5% 68.4%
5wt3A01 3.30.70.2580 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 48.0 4.55e-01 72.7% 61.5%
4qbuA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.69 51.0 4.85e-01 80.0% 84.8%
2h00B00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.69 58.0 3.92e-01 96.4% 28.6%
2vd3A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 53.0 4.86e-01 87.3% 79.7%
2gukA00 3.30.2190.10 Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like 0.68 59.0 4.65e-01 96.4% 48.6%
1i72A00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.68 54.0 3.52e-01 89.1% 33.9%
3bm7A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 47.0 3.84e-01 74.5% 46.2%
3dfeA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 51.0 4.53e-01 87.3% 76.8%
1jg5A00 3.30.1410.10 Alpha Beta › 2-Layer Sandwich › Gtp Cyclohydrolase I Feedback Regulatory Protein; Chain: K › GTP cyclohydrolase I feedback regulatory protein GFRP 0.66 45.0 4.05e-01 74.5% 97.6%
2f4lA03 3.10.28.20 Alpha Beta › Roll › Endonuclease I-creI › Acetamidase/Formamidase-like domains 0.65 52.0 4.71e-01 92.7% 92.5%
3hz7A00 3.30.110.40 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › TusA-like domain 0.64 54.0 5.01e-01 98.2% 75.3%
2djwA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.64 46.0 4.26e-01 80.0% 74.3%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 48.0 4.30e-01 89.1% 69.0%
1j71A01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.63 44.0 3.17e-01 74.5% 98.8%
2od6C00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 48.0 3.97e-01 87.3% 71.0%
1zarA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 50.0 4.43e-01 89.1% 85.2%
5mmjh01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.61 48.0 4.46e-01 92.7% 73.3%
1i6uA01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.61 48.0 4.59e-01 92.7% 82.4%
1zkdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.61 53.0 3.78e-01 100.0% 33.1%
1fg7A02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.61 50.0 3.92e-01 96.4% 45.0%
5flmA02 3.30.1360.140 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.60 48.0 3.74e-01 92.7% 70.6%
4atnA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 49.0 3.52e-01 98.2% 35.2%
2if1A00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.59 43.0 3.49e-01 85.5% 45.2%
4k59A00 2.60.40.4380 Mainly Beta › Sandwich › Immunoglobulin-like › Translational regulator CsrA 0.58 41.0 3.88e-01 74.5% 81.8%
1zo0A00 3.40.630.60 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › 0.58 50.0 3.94e-01 100.0% 50.0%
2pt7G02 3.30.1370.180 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.58 50.0 4.76e-01 98.2% 83.6%
7ovuA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 49.0 3.46e-01 100.0% 85.5%
1yz7A02 3.30.70.1130 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha 0.58 40.0 3.51e-01 74.5% 57.8%
3d2wA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 40.0 3.78e-01 76.4% 62.5%
7n0eB02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.57 46.0 3.78e-01 100.0% 65.6%
2bkkA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.57 43.0 3.84e-01 89.1% 77.8%
2mlgA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 45.0 4.19e-01 100.0% 80.5%
6cc0A01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.55 41.0 3.08e-01 85.5% 67.7%
4feuF01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 41.0 3.85e-01 87.3% 86.3%
4g08A02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.55 39.0 3.63e-01 76.4% 74.3%
1s3jA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 43.0 4.23e-01 100.0% 95.3%
1yyvB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 47.0 3.76e-01 100.0% 51.8%
1p4xA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 43.0 3.51e-01 100.0% 47.2%
1jgsA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 42.0 3.37e-01 100.0% 44.2%
4nb5B01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 43.0 3.87e-01 100.0% 84.7%
3v8hC00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.53 41.0 2.70e-01 92.7% 32.3%
3bz6A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 43.0 3.95e-01 100.0% 80.8%
2dqlA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 42.0 3.50e-01 100.0% 60.9%
2mbfA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 40.0 3.54e-01 100.0% 78.4%
1vr8A00 3.40.1000.20 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › TM1622-like 0.51 40.0 3.20e-01 98.2% 57.0%
2dk5A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 41.0 3.97e-01 100.0% 90.9%
2fl4A02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 41.0 3.47e-01 98.2% 97.1%
3ntvA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 37.0 2.67e-01 87.3% 54.8%
6pcoC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.50 42.0 3.29e-01 100.0% 43.9%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3174952 69.1.1.12 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hom_end 0.81 72.0 5.72e-01 100.0% 52.7%
3206012 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.78 68.0 5.64e-01 100.0% 56.0%
3367254 2003.1.5.154 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_29, Methyltransf_11 0.78 64.0 3.61e-01 89.1% 23.5%
5554 242.1.1.3 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › Hom_end 0.76 67.0 5.42e-01 100.0% 54.7%
4028765 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.76 53.0 4.84e-01 74.5% 54.7%
4935067 304.126.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.76 53.0 4.63e-01 74.5% 49.4%
1388654 242.1.1.1 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.74 65.0 4.63e-01 100.0% 43.3%
5072186 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.74 65.0 5.25e-01 100.0% 59.0%
4026759 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.74 52.0 4.17e-01 74.5% 42.9%
5054678 304.126.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.73 51.0 4.64e-01 74.5% 54.7%
4220147 304.126.1.0 a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.72 50.0 4.39e-01 74.5% 49.4%
4940097 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.72 59.0 5.52e-01 100.0% 74.3%
4225320 306.3.1.4 a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › PFF1_C 0.69 57.0 4.59e-01 90.9% 56.2%
4032021 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.68 58.0 4.81e-01 100.0% 92.4%
3839205 310.3.1.0 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 0.68 58.0 4.62e-01 100.0% 56.7%
5010188 328.5.1.0 a+b two layers › IF3-like › SirA-like › SirA-like 0.68 55.0 5.15e-01 100.0% 71.4%
5620 320.3.1.1 a+b two layers › R3H domain-like › PG1857-like › PG1857-like › DUF2023 0.68 59.0 4.64e-01 96.4% 48.6%
4336258 304.11.1.0 a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.67 55.0 5.09e-01 90.9% 78.6%
3260870 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.64 54.0 4.57e-01 100.0% 56.7%
4213592 3016.1.1.1 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 › Aminotran_1_2 0.62 51.0 4.36e-01 94.5% 56.8%
4561280 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 0.60 48.0 4.08e-01 94.5% 58.0%
4474140 320.2.1.1 a+b two layers › R3H domain-like › Ribosomal protein S8, N-terminal domain › Ribosomal protein S8, N-terminal domain › Ribosomal_S8 0.60 46.0 4.48e-01 92.7% 84.6%
5074782 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.59 45.0 4.00e-01 87.3% 71.8%
3987672 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.57 48.0 4.56e-01 100.0% 80.9%
3279342 101.1.2.135 alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.57 47.0 3.52e-01 100.0% 37.0%
4940569 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 46.0 4.39e-01 100.0% 90.0%
4648749 101.1.2.274 alpha arrays › HTH › HTH › winged helix domain › SgrR_N 0.55 45.0 3.66e-01 100.0% 56.7%
3970872 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.53 39.0 2.76e-01 83.6% 36.6%
3598643 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 43.0 4.05e-01 100.0% 85.7%
3946945 101.1.2.274 alpha arrays › HTH › HTH › winged helix domain › SgrR_N 0.52 41.0 2.89e-01 100.0% 26.5%
4032197 101.1.2.231 alpha arrays › HTH › HTH › winged helix domain › Staph_reg_Sar_Rot 0.51 41.0 3.43e-01 100.0% 56.5%
D2 medium residues 1-95
PDB
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1at0A00 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.82 58.0 4.96e-01 73.7% 49.0%
2lwyA00 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.81 58.0 5.01e-01 100.0% 50.7%
4lx3A00 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.77 56.0 5.49e-01 75.8% 72.3%
1dq3A01 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.74 53.0 4.25e-01 73.7% 55.4%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4994372 69.1.1.0 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint 0.92 58.0 5.27e-01 72.6% 50.8%
4993732 69.1.1.0 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint 0.90 59.0 5.32e-01 74.7% 51.2%
1758564 69.1.1.2 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hom_end_hint 0.82 58.0 4.66e-01 97.9% 40.2%
4950409 69.1.1.0 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint 0.78 57.0 4.71e-01 98.9% 45.8%
4779324 69.1.1.0 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint 0.77 56.0 5.49e-01 75.8% 72.3%
3603291 69.1.1.4 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing 0.72 50.0 4.03e-01 71.6% 39.4%
4821446 69.1.1.0 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint 0.64 57.0 5.26e-01 100.0% 75.8%
D3 medium residues 96-154
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3491040 2496.1.1.0 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like 0.56 35.0 2.82e-01 94.9% 28.5%