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rifoxyc1_full_scaffold_3_prodigal-single.1__X__X__00276

Bact-Vir

rifoxyc1_full_scaffold_3_prodigal-single.1__X__X__00276

Identity

Kingdom:
phage

Quality

66.0 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 165-306
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ot4A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.75 44.0 5.02e-01 84.5% 76.6%
2wyhB04 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.65 38.0 4.48e-01 84.5% 82.2%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.62 38.0 4.44e-01 82.4% 84.5%
1k04A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.62 39.0 4.41e-01 84.5% 83.7%
3kyiA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.59 39.0 4.09e-01 88.7% 72.7%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.59 45.0 4.47e-01 80.3% 92.8%
2y44A00 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.58 47.0 4.33e-01 85.9% 88.0%
6h2dS01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.58 39.0 3.30e-01 95.8% 42.6%
2iaiA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 30.0 3.14e-01 93.7% 53.7%
4bjmC00 1.20.58.1680 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 47.0 4.11e-01 89.4% 80.5%
2wssW01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.56 30.0 3.58e-01 88.7% 75.8%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.56 42.0 4.71e-01 93.7% 97.3%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.55 34.0 4.03e-01 94.4% 96.6%
2r40D00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.55 48.0 4.10e-01 95.8% 82.4%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.54 46.0 4.18e-01 91.5% 76.2%
2f2gA00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.54 45.0 3.98e-01 92.3% 81.9%
5tj5E00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.53 44.0 4.49e-01 94.4% 92.8%
1x9fC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 31.0 3.07e-01 78.9% 53.0%
3frrA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.52 35.0 3.18e-01 87.3% 51.1%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.52 29.0 3.70e-01 90.1% 94.9%
6vq6G02 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 0.51 44.0 4.02e-01 92.3% 80.4%
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.50 40.0 3.30e-01 85.2% 81.3%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.50 40.0 4.11e-01 93.7% 88.7%
4nqiD00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.50 40.0 3.36e-01 83.1% 75.9%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5002845 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.67 47.0 5.08e-01 71.1% 91.7%
3286925 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 0.66 42.0 4.55e-01 83.1% 75.8%
3341807 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.62 33.0 3.72e-01 91.5% 66.4%
3611017 1189.1.1.6 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › ISG65-75 0.60 49.0 3.95e-01 86.6% 78.5%
3444418 3755.4.1.17 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Rx_N 0.55 47.0 4.63e-01 91.5% 85.8%
3965437 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.55 47.0 4.30e-01 91.5% 96.2%
3782377 4177.1.1.9 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Snx8_BAR_dom 0.54 47.0 3.68e-01 91.5% 83.5%
3675237 4177.2.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › Inhibitor of kappaB kinase beta dimerization domain › Inhibitor of kappaB kinase beta dimerization domain 0.54 43.0 3.48e-01 84.5% 70.6%
3503775 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.53 43.0 3.68e-01 85.2% 77.8%
3692483 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.53 45.0 4.26e-01 91.5% 86.5%
4098703 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.52 48.0 3.79e-01 100.0% 58.2%
3715686 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.52 42.0 3.59e-01 87.3% 79.1%
3177702 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.52 41.0 3.48e-01 84.5% 72.3%
3650037 604.1.1.127 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › EMC4 0.51 31.0 3.29e-01 93.7% 66.4%
D2 high residues 336-415
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3k9iA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 38.0 3.48e-01 91.3% 47.6%
1avcA07 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.59 44.0 4.53e-01 88.7% 85.3%
4s3mB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 39.0 3.65e-01 90.0% 54.7%
3nhiA02 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.56 39.0 3.31e-01 73.8% 86.3%
3pvuA02 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.56 38.0 3.86e-01 71.2% 83.7%
2vy1A00 1.10.4180.10 Mainly Alpha › Orthogonal Bundle › Protein LEAFY › Protein LEAFY 0.53 47.0 3.75e-01 100.0% 50.3%
3w2zA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.53 42.0 3.28e-01 86.3% 79.2%
1rsoB00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.52 30.0 3.42e-01 81.2% 76.8%
2rq5A00 1.10.150.60 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › ARID DNA-binding domain 0.52 37.0 3.30e-01 100.0% 50.4%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 40.0 3.03e-01 91.3% 35.5%
2ijqA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.52 38.0 3.23e-01 80.0% 71.0%
1zk8B02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 42.0 3.65e-01 93.8% 82.6%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3968746 3997.1.1.1 ↗ alpha arrays › Helical insertion domain in magnesium chelatase catalytic subunit › Helical insertion domain in magnesium chelatase catalytic subunit › Helical insertion domain in magnesium chelatase catalytic subunit › CobN-Mg_chel 0.68 47.0 3.64e-01 71.2% 33.5%
3271530 4310.1.1.1 ↗ alpha arrays › Dcp2 box A domain › Dcp2 box A domain › Dcp2 box A domain › DCP2 0.59 48.0 4.70e-01 93.8% 86.7%
4023505 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.58 38.0 3.65e-01 77.5% 56.8%
5080860 219.1.1.76 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF553 0.55 47.0 3.61e-01 100.0% 65.4%
3188384 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.54 38.0 3.02e-01 73.8% 82.9%
3645540 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.53 39.0 2.76e-01 77.5% 32.4%
5072615 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.52 37.0 3.44e-01 77.5% 60.0%
3227134 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.52 42.0 3.81e-01 88.7% 73.6%
4129027 7582.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD 0.51 39.0 3.24e-01 86.3% 63.7%
D3 medium residues 482-590
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 44.0 5.14e-01 73.4% 100.0%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 52.0 3.90e-01 86.2% 56.8%
3pwxA01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.62 50.0 4.19e-01 86.2% 81.5%
1wdzA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.62 46.0 3.70e-01 79.8% 88.7%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 46.0 4.32e-01 79.8% 66.2%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.60 30.0 3.69e-01 76.1% 79.4%
4ke2A00 6.10.140.1860 Special › Helix non-globular › Helix Hairpins › 0.59 43.0 3.58e-01 75.2% 42.9%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.58 49.0 3.62e-01 89.9% 76.4%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.57 40.0 4.16e-01 72.5% 86.4%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 42.0 4.24e-01 78.9% 76.9%
7aalA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.57 49.0 3.67e-01 93.6% 83.8%
1w33A00 1.10.3160.10 Mainly Alpha › Orthogonal Bundle › Bbcrasp-1 › Bbcrasp-1 0.55 49.0 4.18e-01 100.0% 89.0%
3syvA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.54 46.0 3.58e-01 93.6% 84.9%
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.52 41.0 4.01e-01 84.4% 83.2%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.51 36.0 3.89e-01 78.9% 86.0%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3298752 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.74 52.0 5.10e-01 77.1% 67.8%
3428852 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.73 46.0 4.27e-01 72.5% 51.1%
4671784 3755.3.1.310 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › CemA 0.66 49.0 4.73e-01 76.1% 69.2%
3611472 524.1.1.1 ↗ alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC 0.65 49.0 4.26e-01 79.8% 66.5%
3967398 3755.1.1.1 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › YscO 0.64 46.0 4.14e-01 76.1% 54.0%
4210642 3755.1.1.12 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › CheZ 0.63 47.0 4.41e-01 77.1% 73.8%
3964578 5094.1.1.1 ↗ a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.61 45.0 4.17e-01 78.0% 77.1%
3437287 5086.1.1.199 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › PF31016 0.60 45.0 3.90e-01 78.9% 60.6%
3973899 5086.1.1.92 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_AprE 0.60 47.0 4.28e-01 83.5% 87.6%
3404270 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.60 47.0 4.49e-01 86.2% 80.8%
4324499 3755.1.1.3 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › SPAM 0.59 44.0 4.03e-01 78.9% 75.9%
3212246 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.56 50.0 4.31e-01 100.0% 92.6%
3410475 4177.1.1.5 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.56 50.0 4.24e-01 100.0% 94.6%
3731259 5042.1.1.1 ↗ extended segments › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › CorA 0.56 50.0 4.26e-01 100.0% 72.1%
3740499 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.55 49.0 3.93e-01 100.0% 87.1%
3962991 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.55 41.0 3.40e-01 79.8% 45.6%
3545387 3602.1.1.0 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain 0.53 36.0 3.68e-01 70.6% 69.1%
4998688 192.2.1.89 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF7121 0.53 40.0 3.10e-01 79.8% 69.4%
4992864 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 0.52 45.0 3.90e-01 90.8% 88.1%
4576287 3755.3.1.471 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Paralemmin 0.52 39.0 3.51e-01 79.8% 70.3%
3931883 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 0.52 38.0 3.88e-01 78.0% 100.0%
4259224 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.51 37.0 3.39e-01 76.1% 55.5%
3244235 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.51 35.0 3.62e-01 74.3% 76.0%
3962942 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.51 43.0 3.86e-01 91.7% 86.7%