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S2_009_000_R2_scaffold_40_prodigal-single.1__X__X__00127

Bact-Vir

S2_009_000_R2_scaffold_40_prodigal-single.1__X__X__00127

Identity

Kingdom:
phage

Quality

71.4 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 3-65
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1jadA00 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.89 82.0 5.36e-01 100.0% 40.1%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.81 65.0 6.79e-01 88.9% 94.7%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.81 66.0 5.26e-01 90.5% 47.2%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.80 69.0 5.33e-01 93.7% 46.3%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.80 60.0 6.44e-01 82.5% 94.3%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.79 56.0 5.85e-01 100.0% 83.9%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.78 70.0 6.46e-01 100.0% 79.5%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 56.0 5.77e-01 77.8% 86.4%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 57.0 5.24e-01 81.0% 64.2%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.74 63.0 5.86e-01 93.7% 81.0%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.74 61.0 4.59e-01 93.7% 38.6%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 55.0 5.62e-01 77.8% 85.0%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 56.0 4.57e-01 82.5% 46.4%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.72 55.0 5.65e-01 92.1% 86.7%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 58.0 5.45e-01 87.3% 75.3%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 55.0 5.18e-01 88.9% 68.4%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.71 57.0 4.71e-01 87.3% 51.8%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 58.0 5.52e-01 92.1% 76.7%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.69 56.0 5.12e-01 87.3% 75.3%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 58.0 5.80e-01 100.0% 90.5%
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 59.0 5.05e-01 98.4% 61.3%
2rbdA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 53.0 4.02e-01 90.5% 35.3%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.68 56.0 5.15e-01 88.9% 71.6%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 59.0 4.73e-01 95.2% 65.3%
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 0.68 59.0 4.25e-01 98.4% 94.5%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.67 54.0 4.75e-01 92.1% 57.7%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.67 48.0 4.69e-01 84.1% 67.6%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.67 59.0 4.99e-01 100.0% 99.1%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 57.0 4.98e-01 93.7% 66.3%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.66 51.0 4.52e-01 87.3% 58.2%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.65 50.0 4.24e-01 84.1% 50.0%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.65 57.0 4.04e-01 100.0% 55.6%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.65 55.0 4.45e-01 100.0% 60.2%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.64 55.0 5.56e-01 98.4% 93.8%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.64 57.0 5.48e-01 100.0% 87.5%
4b3fX01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 55.0 3.51e-01 100.0% 19.1%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.63 54.0 4.80e-01 95.2% 93.3%
4g80T00 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.62 54.0 4.11e-01 98.4% 42.4%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.62 56.0 4.73e-01 100.0% 64.1%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.62 54.0 4.74e-01 95.2% 81.1%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.61 55.0 4.94e-01 98.4% 88.4%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.61 52.0 4.55e-01 100.0% 89.2%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.61 51.0 5.16e-01 98.4% 100.0%
2b5uA02 1.10.287.620 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix Hairpins 0.61 55.0 4.02e-01 100.0% 83.2%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.60 52.0 4.58e-01 98.4% 97.9%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 52.0 5.01e-01 95.2% 88.7%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.60 47.0 4.79e-01 88.9% 90.3%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 52.0 4.97e-01 100.0% 88.0%
2kwhA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 46.0 4.79e-01 84.1% 94.6%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.58 51.0 4.83e-01 100.0% 82.2%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 45.0 3.37e-01 98.4% 48.9%
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.54 47.0 4.36e-01 100.0% 89.2%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3528691 601.19.1.20 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Fy-3 0.89 82.0 6.40e-01 100.0% 79.2%
3970666 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 0.88 82.0 7.68e-01 100.0% 84.0%
3573038 4207.1.1.99 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF28139 0.88 80.0 7.00e-01 98.4% 73.3%
3851320 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.86 75.0 4.72e-01 100.0% 20.8%
5054424 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.85 70.0 6.49e-01 90.5% 76.2%
3756047 192.29.1.243 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Fy-3 0.85 76.0 6.74e-01 100.0% 70.0%
4980095 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.83 75.0 6.28e-01 100.0% 61.0%
4937584 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 74.0 6.99e-01 100.0% 90.7%
4951179 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.82 69.0 5.88e-01 92.1% 63.0%
4828003 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.79 71.0 5.72e-01 100.0% 52.9%
4654983 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.78 57.0 4.69e-01 76.2% 47.3%
4179286 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 0.78 68.0 6.23e-01 100.0% 75.3%
4940229 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 0.75 55.0 3.36e-01 77.8% 17.6%
4075392 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.74 67.0 4.41e-01 100.0% 24.7%
5012157 605.1.1.354 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › MS_channel_1st_1 0.74 64.0 5.88e-01 100.0% 75.3%
3449084 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.73 61.0 5.09e-01 98.4% 54.3%
3282873 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 0.72 61.0 6.12e-01 95.2% 96.8%
3947564 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.72 60.0 5.97e-01 100.0% 87.7%
3906467 1008.1.1.106 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › CSN5_C 0.71 55.0 4.84e-01 82.5% 63.3%
4079591 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 57.0 4.73e-01 87.3% 51.8%
3631949 309.1.2.5 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › Seryl_tRNA_N 0.71 57.0 4.53e-01 87.3% 44.0%
3412019 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.70 59.0 5.29e-01 100.0% 66.7%
4206524 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.70 56.0 4.68e-01 87.3% 50.0%
4042007 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.70 56.0 4.67e-01 88.9% 50.0%
4978412 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.70 59.0 4.20e-01 90.5% 33.7%
4049608 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.70 60.0 4.95e-01 93.7% 54.5%
4957270 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.70 61.0 4.80e-01 100.0% 85.2%
4045132 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 59.0 4.92e-01 96.8% 100.0%
4300676 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.68 57.0 4.70e-01 92.1% 52.7%
4429194 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.68 56.0 4.65e-01 92.1% 51.8%
4210642 3755.1.1.12 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › CheZ 0.67 53.0 4.23e-01 87.3% 43.8%
4555586 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.67 57.0 4.81e-01 93.7% 57.1%
3653791 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.67 57.0 5.39e-01 93.7% 84.0%
3763195 1072.1.1.1 ↗ alpha bundles › Hsp90 co-chaperone Cdc37 N-terminal domain › Hsp90 co-chaperone Cdc37 N-terminal domain › Hsp90 co-chaperone Cdc37 N-terminal domain › CDC37_N 0.67 57.0 4.39e-01 92.1% 45.2%
3968484 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 0.66 56.0 5.38e-01 98.4% 81.4%
3971539 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 0.66 54.0 5.08e-01 87.3% 73.3%
3505608 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 0.66 57.0 5.37e-01 95.2% 82.7%
3725261 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.65 58.0 3.73e-01 100.0% 30.5%
5048093 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.65 58.0 4.82e-01 100.0% 88.2%
5054822 5076.2.1.3 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › DUF4013 0.64 54.0 3.91e-01 100.0% 36.6%
5045310 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 0.64 54.0 5.21e-01 100.0% 81.4%
4263341 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.62 56.0 4.57e-01 100.0% 93.0%
3968144 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 0.62 53.0 5.32e-01 100.0% 92.3%
5050737 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.62 55.0 3.71e-01 100.0% 26.7%
3613914 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 0.61 56.0 5.27e-01 100.0% 88.0%