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amazon_plume_scaffold_4_prodigal-single.1__X__X__00111

Bact-Vir

amazon_plume_scaffold_4_prodigal-single.1__X__X__00111

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 4-61
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.85 54.0 4.54e-01 74.1% 41.8%
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.82 56.0 4.77e-01 77.6% 46.6%
1jadA00 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.81 72.0 4.73e-01 100.0% 25.6%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.81 61.0 4.89e-01 89.7% 43.4%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.81 67.0 6.77e-01 94.8% 93.0%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.80 59.0 6.05e-01 94.8% 82.1%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.78 55.0 4.88e-01 81.0% 53.1%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.76 54.0 4.75e-01 79.3% 51.8%
1i4dA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.75 59.0 4.05e-01 84.5% 83.0%
4i0xG00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 58.0 5.47e-01 86.2% 73.5%
4gzrC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.71 56.0 5.53e-01 87.9% 95.1%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 50.0 4.85e-01 74.1% 82.8%
1wleA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.70 52.0 4.15e-01 79.3% 43.0%
2etnB01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.70 51.0 4.66e-01 79.3% 59.2%
2x2vA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.70 55.0 5.27e-01 87.9% 77.9%
4lunU00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.70 52.0 3.23e-01 79.3% 16.4%
1pd3A00 1.10.287.230 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 49.0 5.05e-01 74.1% 79.6%
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 52.0 4.29e-01 86.2% 45.3%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 60.0 5.40e-01 100.0% 71.8%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.68 55.0 5.04e-01 87.9% 76.6%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.67 56.0 5.32e-01 100.0% 79.7%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.67 52.0 4.76e-01 93.1% 63.4%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 53.0 5.24e-01 86.2% 85.5%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.66 56.0 4.21e-01 100.0% 38.1%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.66 48.0 4.72e-01 79.3% 72.6%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 53.0 4.89e-01 86.2% 87.7%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.65 52.0 4.40e-01 86.2% 52.6%
2bdeA03 1.20.58.1160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 51.0 4.65e-01 86.2% 63.6%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 50.0 4.54e-01 86.2% 62.8%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.64 55.0 4.87e-01 93.1% 95.1%
1dkxA02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 49.0 4.45e-01 82.8% 76.2%
3l1nA01 6.10.140.790 Special › Helix non-globular › Helix Hairpins › 0.64 50.0 5.34e-01 93.1% 96.1%
3h6pC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.64 53.0 5.45e-01 100.0% 98.2%
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 53.0 4.68e-01 93.1% 72.4%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.63 51.0 4.87e-01 86.2% 76.1%
2kg7B00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 53.0 4.60e-01 100.0% 60.8%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 54.0 4.44e-01 93.1% 55.4%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.63 50.0 4.12e-01 86.2% 52.9%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 53.0 4.80e-01 91.4% 71.4%
3buxB01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.63 55.0 4.26e-01 98.3% 63.6%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.62 49.0 4.71e-01 93.1% 75.4%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.62 46.0 4.31e-01 79.3% 71.8%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.61 46.0 4.67e-01 81.0% 82.8%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 51.0 4.88e-01 100.0% 82.4%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.59 46.0 4.83e-01 82.8% 92.3%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 50.0 4.72e-01 93.1% 82.6%
3cbuA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 44.0 3.33e-01 81.0% 51.5%
1wncB00 1.20.5.300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 48.0 4.30e-01 100.0% 66.7%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.57 52.0 3.63e-01 100.0% 33.7%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.57 51.0 4.58e-01 100.0% 72.5%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3388115 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 0.87 79.0 7.07e-01 100.0% 72.5%
4127216 547.1.1.1 ↗ alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.87 80.0 6.24e-01 100.0% 51.3%
4940986 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.86 79.0 6.58e-01 100.0% 65.3%
3246572 3470.1.1.29 ↗ extended segments › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › COPIIcoated_ERV 0.86 78.0 7.31e-01 100.0% 87.1%
4287749 150.5.1.110 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PRESAN 0.85 77.0 6.61e-01 100.0% 77.8%
3281126 3615.1.1.0 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.85 76.0 4.84e-01 100.0% 21.5%
5040843 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.84 75.0 6.36e-01 100.0% 62.1%
4353218 605.1.1.167 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › PKK 0.84 73.0 6.75e-01 98.3% 82.7%
3484887 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.83 75.0 4.60e-01 100.0% 18.1%
4996194 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.83 73.0 6.36e-01 100.0% 65.6%
4951918 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.82 70.0 5.96e-01 96.6% 64.2%
4324592 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.79 70.0 5.84e-01 100.0% 63.0%
5002748 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 0.77 55.0 4.97e-01 79.3% 57.3%
3174080 6169.1.1.0 ↗ extended segments › Transmembrane segment of lysosome-associated membrane glycoprotein 2 › Transmembrane segment of lysosome-associated membrane glycoprotein 2 › Transmembrane segment of lysosome-associated membrane glycoprotein 2 0.76 63.0 5.33e-01 87.9% 97.8%
1877692 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.76 57.0 6.06e-01 87.9% 100.0%
4983374 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.76 66.0 5.13e-01 100.0% 60.0%
3427989 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.76 65.0 6.23e-01 100.0% 84.3%
3212006 601.24.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 0.76 61.0 4.68e-01 87.9% 41.5%
3976071 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.75 67.0 5.79e-01 100.0% 66.7%
3570028 904.1.1.0 ↗ few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain 0.75 64.0 4.57e-01 100.0% 32.0%
3218921 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 0.72 63.0 5.16e-01 100.0% 59.6%
3174635 4207.1.1.102 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF29925 0.72 63.0 5.48e-01 100.0% 78.9%
5001192 3646.1.1.1 ↗ alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.71 60.0 4.26e-01 100.0% 40.5%
3972048 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.71 58.0 5.00e-01 100.0% 57.8%
4683346 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.70 57.0 5.26e-01 93.1% 70.9%
4032308 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.70 59.0 4.30e-01 100.0% 33.5%
4180835 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.69 57.0 5.43e-01 93.1% 80.0%
3644241 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.67 58.0 4.51e-01 94.8% 44.8%
2674763 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.67 56.0 5.27e-01 100.0% 80.0%
4943584 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.67 52.0 4.78e-01 91.4% 63.7%
4247116 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.66 54.0 4.27e-01 86.2% 45.5%
4026 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.66 57.0 4.87e-01 100.0% 60.6%
3569033 3538.1.1.8 ↗ extended segments › MerF › MerF › MerF › PF28754 0.64 55.0 5.68e-01 100.0% 100.0%
172105 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.64 53.0 5.45e-01 100.0% 98.2%
4397870 3456.1.1.1 ↗ extended segments › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › Oxidored_q4 0.64 47.0 3.84e-01 81.0% 46.1%
3962893 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.63 56.0 4.67e-01 100.0% 58.9%
4942789 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 0.62 56.0 4.21e-01 100.0% 63.6%
3253210 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.62 52.0 3.73e-01 100.0% 60.0%
3940780 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 44.0 3.73e-01 93.1% 47.0%
5047384 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 0.59 53.0 5.10e-01 98.3% 89.2%
4200274 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 0.58 49.0 4.14e-01 98.3% 99.0%
3166880 906.1.1.0 ↗ few secondary structure elements › CCCH zinc finger › CCCH zinc finger › CCCH zinc finger 0.58 53.0 4.94e-01 100.0% 94.3%
143217 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 53.0 4.40e-01 100.0% 61.2%
3874058 6158.1.1.0 ↗ alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.58 52.0 4.45e-01 100.0% 95.6%
5000577 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.54 50.0 3.14e-01 100.0% 32.3%
5044800 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 0.50 47.0 4.12e-01 98.3% 83.7%