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rifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00013

Bact-Vir

rifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00013

Identity

Kingdom:
phage

Quality

78.5 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 4-54
PDB
Domain cluster: representative
CATH (62)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.83 71.0 6.52e-01 96.1% 74.2%
2wb7A03 1.20.120.870 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › pT26-6p, five-helical bundle domain 0.82 71.0 5.20e-01 98.0% 47.8%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.82 71.0 5.26e-01 100.0% 42.1%
6h5hA00 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.81 61.0 5.48e-01 88.2% 59.2%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.80 68.0 5.77e-01 98.0% 97.7%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.80 70.0 4.99e-01 100.0% 33.8%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.79 68.0 6.28e-01 98.0% 92.5%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.79 69.0 5.20e-01 98.0% 41.3%
1k04A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.78 67.0 5.41e-01 100.0% 62.5%
3caxA01 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.78 68.0 4.42e-01 98.0% 23.5%
3k17A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.78 66.0 4.86e-01 98.0% 39.3%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.78 69.0 5.08e-01 100.0% 50.0%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.77 67.0 6.38e-01 96.1% 94.9%
2rbdA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.77 67.0 4.81e-01 100.0% 70.7%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.76 63.0 4.84e-01 94.1% 40.3%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.75 66.0 5.60e-01 100.0% 60.0%
2vkzA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.75 66.0 4.17e-01 100.0% 19.5%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 66.0 6.22e-01 100.0% 87.1%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 65.0 5.88e-01 100.0% 76.1%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.74 65.0 4.57e-01 96.1% 34.2%
3qweA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.73 62.0 3.98e-01 100.0% 69.6%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 61.0 5.76e-01 98.0% 77.4%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 60.0 5.00e-01 98.0% 51.0%
1dd3A01 1.20.5.710 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Single helix bin 0.73 52.0 5.09e-01 82.4% 68.4%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 64.0 5.88e-01 96.1% 76.6%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.73 58.0 5.19e-01 92.2% 68.4%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 62.0 4.55e-01 98.0% 36.2%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.72 61.0 5.19e-01 98.0% 57.0%
3pwfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.72 61.0 4.60e-01 98.0% 43.5%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.72 61.0 4.85e-01 98.0% 83.2%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.71 59.0 5.28e-01 96.1% 75.7%
1aueB00 1.20.120.150 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain 0.71 58.0 4.88e-01 100.0% 52.1%
5xtck00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 57.0 4.78e-01 98.0% 50.5%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 51.0 5.35e-01 80.4% 95.3%
4hb1A00 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 0.71 55.0 5.86e-01 88.2% 97.7%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 57.0 5.61e-01 98.0% 93.1%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 59.0 5.31e-01 100.0% 72.4%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 58.0 5.11e-01 100.0% 62.7%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.70 55.0 5.75e-01 88.2% 97.8%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.70 57.0 4.77e-01 92.2% 52.2%
1kpgD00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.70 60.0 3.78e-01 98.0% 83.4%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.69 59.0 4.93e-01 98.0% 63.3%
1jkvA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.69 58.0 3.98e-01 98.0% 25.4%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 61.0 5.80e-01 100.0% 86.7%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.68 57.0 4.44e-01 98.0% 77.4%
3q1pA01 6.10.250.1120 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.68 48.0 5.24e-01 78.4% 100.0%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 55.0 5.38e-01 96.1% 82.8%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 57.0 4.97e-01 100.0% 65.4%
5mmjo00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.67 52.0 4.68e-01 88.2% 65.3%
4kjmB01 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 50.0 4.70e-01 90.2% 66.7%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.67 56.0 4.80e-01 96.1% 78.8%
4fppB01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.66 56.0 5.11e-01 100.0% 73.2%
7tzoA01 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.66 54.0 3.81e-01 98.0% 28.2%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 53.0 4.41e-01 96.1% 53.1%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 53.0 4.96e-01 100.0% 73.5%
8igrI01 2.40.270.10 Mainly Beta › Beta Barrel › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 › DNA-directed RNA polymerase, subunit 2, domain 6 0.65 54.0 3.79e-01 98.0% 69.3%
1f6fA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.65 55.0 3.83e-01 100.0% 55.7%
3e0sA00 1.40.20.10 Mainly Alpha › Alpha solenoid › CHAD domain › CHAD domain 0.65 54.0 3.41e-01 100.0% 33.1%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.63 52.0 4.47e-01 98.0% 54.9%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.62 50.0 4.93e-01 94.1% 91.1%
4wr4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 48.0 4.04e-01 98.0% 53.3%
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.61 50.0 4.43e-01 98.0% 74.7%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4152566 4274.1.1.1 ↗ extended segments › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › MalF_N_TM 0.83 74.0 7.27e-01 100.0% 96.4%
4663376 3593.1.1.1 ↗ a+b complex topology › Oncogenic effector CagA meander beta sheet domain › Oncogenic effector CagA meander beta sheet domain › Oncogenic effector CagA meander beta sheet domain › CagA_N 0.81 70.0 4.13e-01 100.0% 12.8%
5050919 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.79 68.0 5.37e-01 100.0% 56.4%
4123269 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 0.78 67.0 5.36e-01 100.0% 48.6%
5012498 3843.1.1.28 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › MbhD 0.78 62.0 5.78e-01 92.2% 70.8%
3977054 4274.1.1.1 ↗ extended segments › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › MalF_N_TM 0.77 64.0 6.32e-01 96.1% 89.1%
3286104 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.76 64.0 5.21e-01 96.1% 50.0%
3246381 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 0.76 66.0 4.81e-01 98.0% 41.4%
3744275 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 65.0 5.44e-01 94.1% 87.1%
4384750 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 65.0 5.27e-01 96.1% 64.2%
4993041 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.74 62.0 5.43e-01 96.1% 68.8%
4936790 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.74 65.0 5.13e-01 98.0% 56.2%
3487203 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.74 64.0 5.41e-01 98.0% 67.1%
5044025 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.74 62.0 5.34e-01 98.0% 64.7%
5082443 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.74 63.0 4.64e-01 100.0% 44.8%
5006970 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.73 64.0 4.66e-01 98.0% 37.1%
4219218 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 63.0 4.90e-01 96.1% 56.4%
5014075 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.73 62.0 5.11e-01 96.1% 53.3%
4119718 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 63.0 5.24e-01 98.0% 71.1%
5030918 632.11.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.73 60.0 5.26e-01 94.1% 62.5%
5031927 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.72 62.0 5.33e-01 100.0% 61.2%
4018440 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 62.0 5.15e-01 100.0% 75.8%
3520009 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 62.0 5.44e-01 100.0% 72.5%
1141813 159.1.2.2 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG 0.72 59.0 4.86e-01 98.0% 50.0%
4946547 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.72 60.0 4.71e-01 100.0% 42.5%
4076485 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.72 59.0 5.20e-01 100.0% 65.9%
3273862 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.71 61.0 5.06e-01 100.0% 60.0%
4375453 622.4.1.26 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › HisKA 0.71 59.0 5.36e-01 100.0% 68.0%
3237980 2003.1.2.18 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.71 60.0 3.39e-01 98.0% 15.3%
4505128 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 58.0 4.95e-01 96.1% 57.8%
3968647 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 0.71 60.0 5.65e-01 100.0% 83.1%
3386800 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.68 56.0 5.42e-01 98.0% 90.0%
4177393 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 56.0 4.21e-01 100.0% 59.3%
3415494 5029.1.1.0 ↗ extended segments › Oligosaccharyltransferase subunit ost4p › Oligosaccharyltransferase subunit ost4p › Oligosaccharyltransferase subunit ost4p 0.67 56.0 5.38e-01 96.1% 98.3%