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rifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00048

Bact-Vir

rifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00048

Identity

Kingdom:
phage

Quality

85.6 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 3-61
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5fmnA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.93 75.0 6.44e-01 84.7% 58.1%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.93 75.0 6.33e-01 84.7% 55.6%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.92 74.0 6.42e-01 84.7% 58.8%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.92 70.0 7.66e-01 86.4% 97.9%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.91 69.0 5.42e-01 86.4% 41.2%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.90 66.0 7.30e-01 79.7% 95.7%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.89 71.0 6.15e-01 88.1% 58.1%
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 0.89 63.0 7.10e-01 81.4% 100.0%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.87 66.0 6.53e-01 89.8% 77.0%
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.87 80.0 7.27e-01 100.0% 92.1%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.87 71.0 7.02e-01 88.1% 82.3%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.87 76.0 6.88e-01 100.0% 72.7%
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.87 62.0 6.95e-01 91.5% 100.0%
8d3mA02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.87 68.0 4.37e-01 88.1% 20.4%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.86 65.0 6.62e-01 86.4% 82.8%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.85 67.0 6.49e-01 83.1% 90.6%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.84 67.0 4.58e-01 86.4% 26.9%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 64.0 5.31e-01 84.7% 50.0%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.82 75.0 6.42e-01 100.0% 90.0%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.81 62.0 5.88e-01 100.0% 69.0%
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 0.81 72.0 6.07e-01 100.0% 77.6%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 73.0 6.23e-01 100.0% 83.7%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.80 67.0 5.58e-01 89.8% 77.1%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.80 64.0 5.39e-01 88.1% 53.1%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.79 60.0 4.84e-01 84.7% 42.6%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.79 70.0 6.09e-01 100.0% 74.7%
3rc3A05 1.20.58.1080 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 70.0 5.55e-01 100.0% 50.4%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 66.0 5.68e-01 100.0% 81.2%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.76 61.0 6.17e-01 89.8% 91.5%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 66.0 6.32e-01 96.6% 91.2%
6yz2A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.75 62.0 4.97e-01 93.2% 56.7%
2dw4A03 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.75 57.0 4.83e-01 84.7% 60.4%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 56.0 5.19e-01 81.4% 63.2%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 60.0 6.06e-01 91.5% 93.1%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 63.0 5.11e-01 100.0% 77.5%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.73 58.0 5.18e-01 89.8% 61.4%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 55.0 5.50e-01 84.7% 80.6%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 55.0 5.21e-01 84.7% 72.6%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.72 56.0 4.42e-01 88.1% 42.1%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.72 59.0 4.64e-01 91.5% 73.8%
4abxA02 6.10.140.1090 Special › Helix non-globular › Helix Hairpins › 0.71 56.0 5.02e-01 89.8% 63.2%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.71 54.0 4.95e-01 81.4% 68.4%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 54.0 5.10e-01 89.8% 72.0%
4ehsA00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.69 60.0 4.76e-01 100.0% 72.6%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 51.0 4.96e-01 86.4% 72.1%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.68 54.0 5.14e-01 88.1% 72.9%
1rtwB00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.67 58.0 3.92e-01 94.9% 29.8%
8g59R01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.67 58.0 3.81e-01 100.0% 70.2%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.66 57.0 4.37e-01 100.0% 61.4%
1nafA02 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 56.0 5.03e-01 100.0% 80.0%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.64 57.0 3.66e-01 100.0% 38.8%
5mmjb02 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 47.0 4.92e-01 89.8% 100.0%
5mmjn01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 43.0 3.82e-01 81.4% 78.7%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2546344 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.95 76.0 7.58e-01 83.1% 81.7%
4061849 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.95 79.0 6.17e-01 86.4% 46.4%
3954762 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.94 76.0 6.61e-01 84.7% 59.5%
3950461 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.94 76.0 6.17e-01 84.7% 51.0%
3705783 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.94 77.0 6.53e-01 86.4% 56.7%
3575095 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.94 76.0 7.30e-01 84.7% 76.9%
3682710 2004.1.1.529 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, DUF6469 0.93 76.0 4.38e-01 86.4% 11.0%
3779372 220.1.1.115 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_19 0.93 75.0 5.09e-01 84.7% 27.8%
3389693 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.92 75.0 5.54e-01 86.4% 37.8%
3455609 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.91 86.0 6.99e-01 100.0% 71.0%
4507149 4177.1.1.9 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Snx8_BAR_dom 0.91 73.0 4.78e-01 88.1% 22.7%
3221478 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 0.91 75.0 6.10e-01 86.4% 51.0%
3191420 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.91 75.0 7.20e-01 86.4% 78.5%
3326008 5086.1.1.96 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › DUF632 0.91 74.0 6.08e-01 86.4% 51.0%
3602796 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.91 72.0 5.86e-01 83.1% 49.0%
3976486 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.90 72.0 6.14e-01 84.7% 55.6%
3396277 192.17.1.12 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › WHEP-TRS 0.90 70.0 7.00e-01 83.1% 81.7%
3392286 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.90 72.0 5.77e-01 86.4% 46.4%
4026926 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.89 72.0 5.38e-01 86.4% 37.8%
1954342 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.89 74.0 6.33e-01 88.1% 59.6%
3916884 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 0.89 72.0 6.96e-01 86.4% 78.5%
3685099 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 0.88 67.0 6.45e-01 86.4% 72.3%
3928077 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.88 79.0 5.77e-01 96.6% 57.2%
3646784 109.4.1.1407 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › STAG, SCD, HEAT_SCC3-SA 0.88 78.0 4.41e-01 94.9% 17.8%
3225319 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.88 80.0 6.32e-01 100.0% 58.3%
3616328 3826.1.1.41 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › TMEM151 0.87 69.0 5.70e-01 84.7% 50.0%
3738569 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.86 69.0 5.64e-01 86.4% 48.6%
3423402 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.86 67.0 5.95e-01 84.7% 58.8%
3397793 616.1.1.2 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › WHEP-TRS 0.86 67.0 6.89e-01 94.9% 89.1%
4806319 3755.1.1.2 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › YscO-like 0.86 67.0 5.98e-01 84.7% 60.2%
4990095 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.85 67.0 5.89e-01 84.7% 60.0%
3679373 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.85 68.0 6.61e-01 86.4% 78.5%
3318561 616.1.1.2 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › WHEP-TRS 0.85 67.0 6.89e-01 84.7% 90.9%
3932692 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.85 78.0 6.68e-01 100.0% 84.4%
3628598 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.85 76.0 6.86e-01 100.0% 76.2%
3304770 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.84 77.0 5.50e-01 100.0% 45.0%
375927 150.1.1.14 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › EncFtn-like 0.84 68.0 5.77e-01 86.4% 66.3%
3381499 314.1.1.1 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2 0.84 68.0 3.98e-01 88.1% 12.3%
3399433 3826.1.1.39 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › WHEP-TRS 0.83 66.0 6.21e-01 84.7% 71.4%
4951559 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 65.0 6.00e-01 86.4% 97.3%
3605626 192.12.1.0 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM 0.82 77.0 6.15e-01 100.0% 77.1%
3814372 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 0.81 63.0 5.18e-01 84.7% 50.5%
3386373 605.1.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.79 64.0 6.26e-01 89.8% 87.7%
3403179 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.79 70.0 5.68e-01 96.6% 88.6%
3573559 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.77 70.0 5.47e-01 100.0% 69.2%
1506772 3812.1.1.1 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › T3SS_needle_E 0.76 67.0 6.35e-01 98.3% 92.9%
2898272 3812.1.1.1 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › T3SS_needle_E 0.76 67.0 6.30e-01 100.0% 93.1%
3838316 3567.1.1.150 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › H-kinase_dim 0.75 59.0 5.53e-01 88.1% 86.7%
5052725 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.75 64.0 6.05e-01 94.9% 87.1%
3489528 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 61.0 4.56e-01 100.0% 41.9%
4030521 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.63 52.0 4.85e-01 100.0% 73.3%