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LD_Run2_08_scaffold_35_prodigal-single.1__X__X__00109

Bact-Vir

LD_Run2_08_scaffold_35_prodigal-single.1__X__X__00109

Identity

Kingdom:
phage

Quality

86.9 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 6-65
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.87 67.0 5.14e-01 81.7% 70.4%
3eslA01 1.20.58.2070 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 68.0 6.29e-01 93.3% 80.0%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 62.0 6.34e-01 83.3% 89.5%
1sxjB03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.80 67.0 5.75e-01 91.7% 73.9%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.78 58.0 4.66e-01 80.0% 58.1%
3fy6A01 3.30.2210.10 Alpha Beta › 2-Layer Sandwich › Integron cassette protein fold › Integron cassette protein superfamily 0.78 54.0 4.36e-01 71.7% 41.1%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.77 61.0 6.30e-01 85.0% 91.1%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.77 53.0 5.13e-01 78.3% 65.2%
6ircA01 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.76 57.0 3.88e-01 80.0% 24.1%
3ismC01 1.25.40.240 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ku, C-terminal domain 0.76 68.0 4.96e-01 98.3% 39.6%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.75 62.0 5.98e-01 90.0% 98.5%
2p4vA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.74 58.0 5.35e-01 83.3% 81.6%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.74 57.0 5.28e-01 83.3% 64.9%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.73 57.0 5.04e-01 85.0% 65.5%
3akjA02 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.73 61.0 4.17e-01 91.7% 74.1%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.70 53.0 3.97e-01 83.3% 64.5%
4gzrC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.70 48.0 4.81e-01 73.3% 83.6%
1ldjA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.69 54.0 4.36e-01 85.0% 67.8%
3rkgA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.69 59.0 4.39e-01 100.0% 68.9%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.68 51.0 5.09e-01 83.3% 81.0%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.68 52.0 5.16e-01 83.3% 85.5%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.67 51.0 4.13e-01 85.0% 42.7%
8sppA01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.67 58.0 3.59e-01 100.0% 37.4%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.67 57.0 3.94e-01 96.7% 87.7%
1lfkA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.66 59.0 3.54e-01 96.7% 18.7%
1s7oB00 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 0.66 50.0 4.08e-01 80.0% 59.0%
2rkkA01 1.25.40.270 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 0.66 58.0 4.30e-01 100.0% 39.7%
2co9A00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.65 49.0 4.13e-01 81.7% 75.5%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.65 58.0 5.16e-01 100.0% 85.9%
2v6kA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 53.0 4.17e-01 93.3% 66.9%
1cmjA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.62 54.0 3.26e-01 96.7% 18.5%
2js9A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.62 48.0 4.49e-01 90.0% 69.1%
1z1vA00 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.61 44.0 4.21e-01 83.3% 65.7%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.61 53.0 4.39e-01 100.0% 66.1%
6b8hO01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.61 44.0 3.83e-01 80.0% 54.5%
1gt0D00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.58 44.0 4.00e-01 81.7% 82.3%
2p0wA03 1.10.10.390 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.56 42.0 4.43e-01 88.3% 90.7%
3s64A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.56 47.0 4.36e-01 96.7% 79.0%
1onwA02 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.56 47.0 3.08e-01 93.3% 21.1%
1g2rA00 3.30.1230.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › YlxR-like 0.56 47.0 4.14e-01 98.3% 74.5%
1irxA04 1.10.10.770 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.54 47.0 3.89e-01 98.3% 79.6%
2ky4A01 1.10.3130.20 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › Phycobilisome linker domain 0.53 42.0 3.38e-01 91.7% 79.4%
3s63A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.53 41.0 3.74e-01 91.7% 67.0%
3vldA02 1.25.40.580 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 45.0 3.35e-01 95.0% 61.4%
1vt0k00 1.10.3230.20 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › P22 tail accessory factor (Gp4) 0.53 45.0 3.50e-01 100.0% 75.2%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4034213 632.2.1.5 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1542 0.87 66.0 5.94e-01 80.0% 60.0%
3720226 3860.1.1.0 alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm 0.85 67.0 5.03e-01 83.3% 45.9%
3717826 547.1.1.0 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain 0.85 67.0 5.46e-01 83.3% 59.0%
4031490 632.2.1.5 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1542 0.85 64.0 5.93e-01 80.0% 64.0%
4177809 4990.1.1.1 alpha arrays › Lipase chaperone LifO-like › Lipase chaperone LifO-like › Lipase chaperone LifO-like › Lipase_chap 0.85 73.0 4.65e-01 95.0% 21.1%
4460746 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.83 74.0 5.15e-01 98.3% 95.0%
4235299 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.82 75.0 5.18e-01 100.0% 92.9%
5074225 604.5.1.0 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.81 73.0 6.31e-01 100.0% 95.6%
4112673 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.80 74.0 5.13e-01 100.0% 94.9%
3924719 371.1.1.0 few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.80 71.0 6.06e-01 98.3% 71.6%
3715395 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.79 60.0 5.71e-01 81.7% 77.1%
5042653 138.1.1.2 alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › Rep_fac_C 0.78 65.0 5.52e-01 90.0% 72.6%
3582573 192.24.1.0 alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain 0.78 60.0 4.88e-01 83.3% 85.5%
4964387 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.77 57.0 4.77e-01 78.3% 51.0%
5046799 10.13.1.10 beta sandwiches › jelly-roll › Calcium ATPase, transduction domain A › Calcium ATPase, transduction domain A › Cation_ATPase_C 0.77 58.0 3.34e-01 81.7% 9.1%
5004436 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 64.0 4.56e-01 93.3% 34.1%
4011398 633.24.1.0 alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain 0.76 62.0 5.54e-01 91.7% 81.2%
4043979 3812.1.1.4 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › GrpE 0.75 55.0 5.56e-01 85.0% 78.3%
4034449 109.28.1.1 alpha superhelices › Repetitive alpha hairpins › EssB extracellular domain › EssB extracellular domain › YukC 0.73 62.0 4.70e-01 96.7% 43.3%
3995656 106.1.1.1 alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.73 65.0 4.78e-01 100.0% 89.4%
5001312 632.15.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.73 52.0 4.78e-01 76.7% 87.5%
4964864 148.1.3.404 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › PrkA 0.73 63.0 4.34e-01 100.0% 35.8%
3423910 6155.1.1.0 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.70 60.0 4.75e-01 98.3% 63.8%
3711338 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 57.0 3.73e-01 93.3% 43.6%
3927392 198.1.1.1 alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2 0.70 58.0 5.29e-01 91.7% 68.8%
3930816 101.1.2.236 alpha arrays › HTH › HTH › winged helix domain › POLR3C_WHD 0.69 53.0 3.44e-01 83.3% 31.3%
4029559 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 60.0 4.35e-01 100.0% 73.1%
3959510 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.69 59.0 3.53e-01 100.0% 13.5%
3740780 604.12.1.2 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.68 60.0 5.56e-01 98.3% 96.0%
4003615 5054.1.1.59 alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans, Ion_trans_2 0.68 50.0 3.45e-01 83.3% 21.8%
3223457 101.1.2.661 alpha arrays › HTH › HTH › winged helix domain › HTH_9, POLR3C_WHD 0.67 52.0 3.42e-01 86.7% 63.6%
3954713 2008.1.1.59 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.67 57.0 3.81e-01 100.0% 24.3%
3717521 206.1.1.70 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.67 57.0 3.60e-01 98.3% 74.8%
5018387 604.18.1.0 alpha bundles › Spectrin repeat-like › Triple-helical domain in regulatory ATPase variant A (RavA) › Triple-helical domain in regulatory ATPase variant A (RavA) 0.67 58.0 4.90e-01 100.0% 100.0%
5004431 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.65 57.0 3.77e-01 96.7% 45.8%
3202292 101.38.1.3 alpha arrays › HTH › DNA-binding domain of the replication initiator protein ColE2-Rep › DNA-binding domain of the replication initiator protein ColE2-Rep › DUF6891 0.65 56.0 5.40e-01 100.0% 91.4%
4594071 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.65 57.0 5.13e-01 100.0% 88.2%
4817720 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.65 49.0 3.15e-01 83.3% 17.1%
3731112 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.64 49.0 4.98e-01 85.0% 83.3%
5026055 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.64 54.0 3.50e-01 96.7% 50.2%
4567807 397.7.1.6 few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 › PF29718 0.64 53.0 5.21e-01 91.7% 95.4%
3717721 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.64 54.0 3.58e-01 96.7% 25.3%
3391605 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.63 56.0 5.47e-01 98.3% 98.5%
350072 198.1.1.1 alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2 0.62 50.0 4.58e-01 91.7% 72.8%
5001690 3276.1.1.0 alpha arrays › N-terminal domain in MogR repressor › N-terminal domain in MogR repressor › N-terminal domain in MogR repressor 0.62 54.0 5.14e-01 100.0% 87.1%
5005257 2.21.1.0 beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) 0.61 53.0 3.87e-01 100.0% 35.3%
3931210 191.1.1.0 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.61 53.0 4.51e-01 100.0% 68.0%
3915549 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.60 48.0 4.44e-01 88.3% 68.4%
147354 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.56 47.0 4.36e-01 96.7% 79.0%
4936146 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.55 46.0 4.77e-01 91.7% 100.0%
3238440 101.1.1.21 alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_Tc5 0.52 38.0 3.80e-01 85.0% 89.2%
4928737 592.2.1.0 alpha arrays › PWI domain-like › YugE-like › YugE-like 0.51 39.0 3.51e-01 90.0% 66.3%