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rifoxya1_full_scaffold_1_prodigal-single.1__X__X__00306

Bact-Vir

rifoxya1_full_scaffold_1_prodigal-single.1__X__X__00306

Identity

Kingdom:
phage

Quality

78.2 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 1-48
PDB
Domain cluster: representative
CATH (66)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2okuA00 1.20.120.470 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Acyl-CoA dehydrogenase, C-terminal domain 0.92 83.0 6.05e-01 100.0% 39.3%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.84 66.0 5.95e-01 85.4% 81.5%
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 0.84 74.0 5.83e-01 100.0% 63.3%
2ch7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.83 73.0 4.41e-01 100.0% 85.8%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.83 72.0 5.22e-01 100.0% 66.2%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.82 67.0 5.80e-01 93.8% 100.0%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 69.0 6.04e-01 100.0% 76.3%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.81 70.0 5.38e-01 100.0% 46.4%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 70.0 5.51e-01 100.0% 48.0%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.80 69.0 6.54e-01 100.0% 83.1%
1qu7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.80 68.0 4.39e-01 100.0% 24.2%
3rauA00 1.25.40.280 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › alix/aip1 like domains 0.80 69.0 4.10e-01 100.0% 13.7%
4abyD00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.80 67.0 4.01e-01 97.9% 14.5%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 65.0 5.22e-01 100.0% 77.5%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.78 65.0 6.15e-01 100.0% 85.2%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 66.0 5.67e-01 100.0% 67.9%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 65.0 4.53e-01 100.0% 28.6%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.78 64.0 5.96e-01 97.9% 88.9%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.77 65.0 5.50e-01 100.0% 58.8%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.77 66.0 5.52e-01 100.0% 75.3%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.76 57.0 5.42e-01 83.3% 100.0%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.76 65.0 5.40e-01 100.0% 55.1%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 65.0 5.19e-01 100.0% 48.5%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.76 64.0 5.72e-01 100.0% 67.1%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.76 64.0 5.91e-01 100.0% 93.8%
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.76 63.0 5.42e-01 100.0% 66.3%
2a2fX02 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.75 63.0 4.65e-01 97.9% 35.7%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 62.0 5.64e-01 100.0% 71.8%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.75 63.0 5.48e-01 100.0% 64.6%
2clbA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.74 61.0 4.37e-01 100.0% 30.8%
3urzA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.74 63.0 4.23e-01 100.0% 24.8%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.74 60.0 5.11e-01 100.0% 81.1%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.74 60.0 5.65e-01 100.0% 81.2%
3fb2A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 61.0 4.90e-01 100.0% 46.7%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 59.0 5.22e-01 100.0% 61.7%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.73 59.0 5.27e-01 93.8% 90.4%
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.73 62.0 4.72e-01 100.0% 42.0%
3hhcC00 1.20.1250.60 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interferon lambda 0.73 59.0 4.33e-01 100.0% 31.8%
4akgA04 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.73 59.0 4.28e-01 100.0% 31.4%
2wmmA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.72 59.0 5.90e-01 100.0% 95.9%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.72 59.0 5.16e-01 100.0% 59.3%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.72 59.0 4.82e-01 100.0% 99.0%
5ejrA01 1.25.40.530 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › MyTH4 domain 0.72 54.0 3.63e-01 89.6% 20.4%
3k6tB00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 56.0 5.62e-01 97.9% 89.8%
2bl2A00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.71 58.0 4.20e-01 100.0% 32.7%
4dyqA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.70 59.0 4.73e-01 100.0% 46.6%
4wqoD00 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.70 60.0 4.35e-01 97.9% 66.0%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 58.0 5.44e-01 100.0% 87.3%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.70 60.0 4.06e-01 97.9% 94.0%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.70 56.0 5.22e-01 95.8% 100.0%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 55.0 5.00e-01 95.8% 68.5%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.70 57.0 3.41e-01 100.0% 12.4%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 55.0 4.93e-01 100.0% 61.5%
1rq5A02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.68 56.0 3.25e-01 100.0% 20.4%
6fakA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.68 56.0 4.83e-01 95.8% 63.0%
1x0tA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.67 52.0 4.99e-01 93.8% 73.8%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.67 56.0 4.86e-01 100.0% 59.8%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 54.0 4.90e-01 100.0% 67.2%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.64 50.0 4.46e-01 100.0% 57.3%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.64 49.0 4.06e-01 100.0% 43.6%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.63 52.0 4.34e-01 100.0% 62.5%
3fkjA02 1.10.10.2240 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.63 44.0 4.01e-01 93.8% 56.2%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.62 53.0 4.13e-01 100.0% 45.0%
3dv8A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 51.0 3.76e-01 97.9% 55.4%
1vibA00 1.10.287.120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Neurotoxin B-IV-like 0.62 50.0 4.87e-01 97.9% 87.3%
4ehsA00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.61 45.0 3.58e-01 91.7% 36.3%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2663455 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.88 78.0 6.93e-01 100.0% 70.6%
3258825 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.85 74.0 4.31e-01 100.0% 13.4%
3737161 3559.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Med22 0.85 75.0 5.68e-01 100.0% 43.6%
1157010 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.84 73.0 5.83e-01 100.0% 49.0%
5006936 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 0.84 72.0 6.60e-01 100.0% 73.8%
166728 150.1.1.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF305 0.83 72.0 5.05e-01 100.0% 33.1%
4095641 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.82 70.0 5.70e-01 100.0% 51.6%
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 0.82 70.0 6.14e-01 100.0% 69.3%
2893266 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.81 71.0 5.79e-01 100.0% 56.5%
3877354 3291.1.1.14 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › LAP2alpha 0.81 69.0 4.61e-01 100.0% 24.6%
3680604 246.3.1.17 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › PF27823 0.81 69.0 4.25e-01 100.0% 18.2%
3485413 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.79 64.0 6.36e-01 100.0% 88.0%
4025064 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.79 67.0 6.15e-01 97.9% 78.5%
3837413 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 0.79 67.0 4.78e-01 100.0% 32.0%
3287592 3443.1.1.0 ↗ alpha duplicates or obligate multimers › Get5 carboxyl domain › Get5 carboxyl domain › Get5 carboxyl domain 0.79 63.0 6.29e-01 100.0% 90.0%
3606827 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.78 67.0 6.69e-01 100.0% 98.0%
4595635 148.1.3.26 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_9 0.77 64.0 4.56e-01 100.0% 31.2%
3456370 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.77 65.0 4.64e-01 100.0% 31.0%
3958574 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 0.77 65.0 4.55e-01 100.0% 100.0%
4500653 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.77 64.0 4.59e-01 100.0% 48.7%
3631342 3559.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Med22 0.76 64.0 5.08e-01 100.0% 45.7%
3701245 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.76 63.0 5.00e-01 100.0% 44.5%
4438700 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.76 64.0 5.43e-01 100.0% 58.8%
4882209 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 0.76 63.0 5.38e-01 100.0% 56.5%
4536213 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.76 64.0 4.16e-01 100.0% 23.6%
4954895 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 0.75 63.0 5.22e-01 100.0% 52.2%
3698336 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.75 62.0 5.31e-01 100.0% 56.5%
3291685 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 0.75 62.0 4.37e-01 100.0% 29.4%
5057918 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.75 61.0 3.79e-01 100.0% 15.3%
4529282 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 60.0 5.08e-01 100.0% 58.9%
3445040 3826.1.1.53 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Rx_N 0.73 62.0 5.22e-01 100.0% 58.8%
3503635 605.1.1.133 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › OST3_OST6 0.73 60.0 4.63e-01 100.0% 40.8%
4945610 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.72 58.0 4.77e-01 100.0% 62.0%
3187479 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.71 60.0 5.01e-01 100.0% 66.7%
3497751 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 0.71 58.0 4.98e-01 100.0% 56.5%
4801882 192.1.1.1 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › MCPsignal 0.69 56.0 5.24e-01 100.0% 100.0%
4973584 604.3.1.51 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › 8xMP 0.67 54.0 4.67e-01 100.0% 67.0%
3589723 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 57.0 4.27e-01 100.0% 62.4%
144301 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.66 55.0 4.96e-01 100.0% 67.1%