←Back to structures

S2_018_000_R2_scaffold_9_prodigal-single.1__X__X__00019

Bact-Vir

S2_018_000_R2_scaffold_9_prodigal-single.1__X__X__00019

Identity

Kingdom:
phage

Quality

71.1 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 4-79
PDB
Domain cluster: representative
CATH (62)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.86 68.0 6.69e-01 84.2% 80.2%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.82 74.0 5.70e-01 100.0% 45.8%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.82 74.0 6.49e-01 100.0% 71.4%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.81 64.0 6.85e-01 89.5% 98.5%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 66.0 6.13e-01 88.2% 71.9%
4mh6A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 70.0 5.41e-01 97.4% 44.7%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.80 61.0 6.56e-01 86.8% 96.9%
2dw4A03 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.80 72.0 6.49e-01 98.7% 90.1%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.80 67.0 6.98e-01 90.8% 97.2%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.79 72.0 6.38e-01 100.0% 79.4%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.79 71.0 5.67e-01 100.0% 51.0%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.79 69.0 6.25e-01 100.0% 72.5%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 61.0 6.57e-01 88.2% 100.0%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.78 65.0 5.97e-01 92.1% 70.4%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 65.0 6.26e-01 92.1% 84.9%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.78 56.0 5.35e-01 84.2% 65.2%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.78 56.0 5.18e-01 84.2% 59.8%
2rd0B00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 69.0 5.67e-01 100.0% 59.0%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 66.0 6.62e-01 97.4% 92.3%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.77 63.0 6.48e-01 92.1% 98.6%
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 65.0 5.76e-01 92.1% 67.9%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 63.0 5.80e-01 98.7% 69.6%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.76 64.0 5.69e-01 96.1% 64.5%
5y06A01 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 67.0 4.73e-01 100.0% 32.8%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.76 59.0 6.29e-01 85.5% 100.0%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.76 56.0 6.16e-01 82.9% 100.0%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.76 67.0 6.40e-01 100.0% 93.3%
4ke2A00 6.10.140.1860 Special › Helix non-globular › Helix Hairpins › 0.74 67.0 4.94e-01 100.0% 98.5%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.74 62.0 6.08e-01 92.1% 87.7%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 58.0 6.02e-01 85.5% 95.7%
2kwhA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 51.0 5.64e-01 75.0% 98.2%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.73 58.0 5.64e-01 88.2% 87.2%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 61.0 6.01e-01 93.4% 87.7%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.73 64.0 6.52e-01 97.4% 100.0%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.73 63.0 5.74e-01 100.0% 75.5%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 52.0 5.63e-01 92.1% 93.5%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.72 64.0 5.55e-01 98.7% 67.5%
2bdeA03 1.20.58.1160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 61.0 6.16e-01 96.1% 93.5%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.72 58.0 5.46e-01 97.4% 72.2%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 64.0 5.75e-01 97.4% 74.8%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.72 55.0 4.35e-01 81.6% 100.0%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 52.0 5.52e-01 98.7% 92.2%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 52.0 5.19e-01 81.6% 76.9%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.70 59.0 6.03e-01 100.0% 98.6%
1s35A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 58.0 5.31e-01 92.1% 70.3%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.70 50.0 5.48e-01 86.8% 100.0%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.69 64.0 5.88e-01 100.0% 85.4%
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 0.69 52.0 4.44e-01 80.3% 52.0%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.69 58.0 5.69e-01 96.1% 100.0%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.68 57.0 5.62e-01 92.1% 88.7%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 59.0 5.35e-01 100.0% 72.0%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.67 43.0 4.81e-01 71.1% 87.5%
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.67 56.0 5.38e-01 93.4% 80.7%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.67 51.0 4.77e-01 88.2% 66.7%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.67 57.0 5.73e-01 94.7% 97.4%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.66 44.0 4.48e-01 78.9% 69.7%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.65 48.0 5.14e-01 82.9% 100.0%
2h7oA02 1.20.58.1230 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Rac1-binding domain, C-terminal subdomain 0.64 51.0 4.20e-01 90.8% 69.4%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.62 49.0 4.44e-01 88.2% 62.7%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.62 50.0 4.92e-01 92.1% 83.5%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.60 48.0 4.51e-01 96.1% 71.9%
4m52A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 47.0 3.44e-01 98.7% 54.5%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4981185 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.89 83.0 6.14e-01 100.0% 76.6%
3597345 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.86 79.0 6.82e-01 100.0% 72.2%
3980443 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 0.86 69.0 5.90e-01 85.5% 67.0%
4978412 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.85 69.0 5.19e-01 89.5% 37.7%
4959086 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 0.84 72.0 7.31e-01 93.4% 96.0%
3212195 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.83 72.0 6.31e-01 98.7% 64.5%
4210642 3755.1.1.12 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › CheZ 0.82 75.0 6.19e-01 100.0% 87.7%
3366371 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.81 73.0 4.95e-01 100.0% 28.5%
3543713 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.80 73.0 6.86e-01 98.7% 92.2%
3990182 3922.1.1.226 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Fy-3 0.80 71.0 6.23e-01 100.0% 73.0%
3386594 3291.1.1.197 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › MCPsignal 0.80 72.0 6.42e-01 100.0% 72.4%
3456370 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.79 72.0 5.63e-01 100.0% 72.3%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.79 71.0 6.06e-01 100.0% 63.9%
4106620 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.78 66.0 6.67e-01 93.4% 100.0%
3402340 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.78 70.0 4.75e-01 100.0% 34.8%
3505608 192.29.1.1 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB_dom 0.78 69.0 6.97e-01 98.7% 100.0%
4945751 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.78 72.0 6.26e-01 100.0% 70.0%
3476064 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.77 69.0 5.94e-01 100.0% 66.7%
4043484 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.77 70.0 6.15e-01 100.0% 74.5%
3521054 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.76 68.0 5.06e-01 100.0% 74.7%
3198228 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 69.0 4.99e-01 100.0% 39.0%
3911413 148.1.3.13 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_9 0.76 68.0 4.47e-01 100.0% 25.2%
1879027 244.1.1.6 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.75 66.0 4.21e-01 100.0% 24.4%
3719904 148.1.3.13 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_9 0.75 66.0 4.25e-01 100.0% 21.9%
3947741 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.75 66.0 5.72e-01 100.0% 65.0%
3634125 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.74 54.0 5.93e-01 93.4% 98.3%
3592972 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.74 66.0 4.89e-01 100.0% 46.7%
4042007 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 66.0 5.85e-01 100.0% 76.4%
3733140 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.74 65.0 5.13e-01 97.4% 51.0%
4043561 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 65.0 5.77e-01 100.0% 76.4%
3903553 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.71 58.0 5.05e-01 88.2% 59.1%
2636645 192.15.1.2 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Mod_r 0.70 54.0 5.70e-01 86.8% 97.0%
3471229 148.1.3.13 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_9 0.70 61.0 4.08e-01 100.0% 25.7%
3719551 6111.1.1.0 ↗ a+b complex topology › C-terminal domain of cytoplasmic dynein heavy chain › C-terminal domain of cytoplasmic dynein heavy chain › C-terminal domain of cytoplasmic dynein heavy chain 0.70 60.0 3.40e-01 100.0% 8.2%
3699451 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.68 60.0 5.29e-01 100.0% 66.1%
4938211 5076.2.1.17 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › AI-2E_transport 0.66 58.0 4.13e-01 97.4% 34.2%
3573038 4207.1.1.99 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF28139 0.66 51.0 4.86e-01 93.4% 71.1%
5030596 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.65 50.0 5.24e-01 89.5% 100.0%
3236471 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.65 58.0 3.97e-01 100.0% 37.5%
3784055 192.24.1.0 ↗ alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain 0.65 55.0 4.75e-01 100.0% 62.3%
3785340 7581.1.1.3 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › ketoacyl-synt,Ketoacyl-synt_C 0.62 54.0 3.13e-01 98.7% 30.7%
3494616 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.61 50.0 4.88e-01 92.1% 84.7%