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js4906-29-5_S40_scaffold_9_prodigal-single.1__X__X__00085

Bact-Vir

js4906-29-5_S40_scaffold_9_prodigal-single.1__X__X__00085

Identity

Kingdom:
phage

Quality

79.7 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 17-91
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12666.13 best PrgI 44.4 2.90e-11 100.0% 78.0%
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bjbD00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.77 52.0 3.93e-01 70.7% 32.8%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.76 51.0 4.13e-01 70.7% 37.7%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.73 52.0 3.30e-01 76.0% 39.6%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.72 53.0 4.57e-01 80.0% 50.0%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.72 52.0 5.28e-01 81.3% 77.0%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.70 50.0 4.86e-01 78.7% 68.3%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.69 51.0 4.90e-01 80.0% 68.2%
2oauA01 1.10.287.1260 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 57.0 5.16e-01 93.3% 66.7%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.67 48.0 4.88e-01 76.0% 75.0%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.67 53.0 3.55e-01 85.3% 56.6%
2dg7A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.67 48.0 3.66e-01 94.7% 31.2%
5jqkA03 3.90.230.10 Alpha Beta › Alpha-Beta Complex › Creatine Amidinohydrolase › Creatinase/methionine aminopeptidase superfamily 0.67 47.0 3.16e-01 74.7% 33.4%
4xomB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.67 55.0 3.93e-01 88.0% 44.9%
1h3lB00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.66 42.0 4.24e-01 76.0% 62.8%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.66 53.0 5.13e-01 90.7% 77.6%
2a2fX01 1.10.357.30 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Exocyst complex subunit Sec15 C-terminal domain, N-terminal subdomain 0.65 54.0 4.15e-01 90.7% 53.9%
6m36O01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.63 47.0 4.32e-01 78.7% 86.5%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.63 41.0 4.17e-01 74.7% 69.4%
2g2dA00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.63 49.0 3.83e-01 84.0% 80.0%
1jt6A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.62 42.0 3.49e-01 70.7% 40.1%
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.62 41.0 3.77e-01 88.0% 50.5%
6k9pB02 1.20.1300.20 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Peptidase C65 Otubain, subdomain 2 0.60 43.0 3.50e-01 77.3% 38.2%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.60 42.0 3.88e-01 73.3% 59.8%
2uxwA04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.59 46.0 3.90e-01 86.7% 68.5%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.58 46.0 4.07e-01 89.3% 63.8%
1t72A01 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 0.58 43.0 3.68e-01 78.7% 50.4%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 43.0 4.59e-01 81.3% 96.8%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.57 39.0 4.17e-01 72.0% 87.7%
1pixA03 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.57 43.0 3.01e-01 86.7% 41.5%
2ddhA04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.57 47.0 4.03e-01 96.0% 87.9%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.57 42.0 4.47e-01 78.7% 95.2%
7kfuC02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.56 44.0 3.16e-01 86.7% 39.5%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.56 42.0 4.13e-01 80.0% 88.9%
2v6eA01 1.10.287.3180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 38.0 3.86e-01 73.3% 72.0%
4nqwA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 38.0 3.98e-01 73.3% 98.4%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 39.0 3.90e-01 80.0% 74.4%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.54 40.0 3.70e-01 80.0% 62.6%
3ayhA00 1.20.1250.40 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › RNA Polymerase II, Rpb4 subunit 0.53 36.0 3.00e-01 70.7% 84.3%
1r1dA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 43.0 2.96e-01 90.7% 36.4%
2pusA04 6.10.140.300 Special › Helix non-globular › Helix Hairpins › 0.50 39.0 3.56e-01 88.0% 100.0%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1380704 191.1.1.60 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_20 0.77 53.0 4.54e-01 70.7% 46.1%
3686609 6026.1.1.0 alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.77 55.0 5.15e-01 76.0% 62.2%
3483031 130.1.1.0 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.76 55.0 6.08e-01 82.7% 95.0%
4016157 6026.1.1.1 alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.75 55.0 4.48e-01 89.3% 43.0%
3903917 5058.1.1.17 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › NRN1 0.74 51.0 4.88e-01 70.7% 62.4%
3950890 5063.1.1.0 alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK 0.73 55.0 5.97e-01 84.0% 100.0%
3392260 6026.1.1.0 alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.73 56.0 5.83e-01 84.0% 87.1%
5047182 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 0.73 56.0 5.99e-01 90.7% 95.4%
3589830 5043.2.1.8 extended segments › Sensor proteins transmembrane domains › NarQ transmembrane domain › NarQ transmembrane domain › DUF5592 0.73 58.0 6.04e-01 94.7% 94.3%
4419476 4958.1.1.1 a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 0.73 52.0 3.93e-01 76.0% 32.0%
4981035 5058.1.1.16 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_1 0.73 56.0 6.01e-01 90.7% 95.4%
3973031 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 0.72 61.0 5.33e-01 93.3% 61.8%
4317794 5058.1.1.1 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_1,MS_channel_1st 0.72 60.0 5.27e-01 88.0% 63.8%
3952366 4970.1.1.0 alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.72 54.0 5.85e-01 84.0% 100.0%
3231673 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.71 47.0 4.75e-01 72.0% 68.0%
4076608 109.4.1.924 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_CcmH_CycH 0.71 52.0 3.45e-01 85.3% 19.7%
3764064 4009.1.1.0 alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.71 52.0 4.99e-01 82.7% 68.2%
2647290 225.1.1.6 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_2 0.71 47.0 4.65e-01 74.7% 63.7%
3463858 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.71 48.0 4.38e-01 72.0% 53.0%
5028558 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 0.71 62.0 5.58e-01 98.7% 71.0%
4998576 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.71 51.0 5.18e-01 77.3% 84.0%
5053821 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.70 46.0 4.25e-01 81.3% 51.0%
3643105 6026.1.1.1 alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.70 52.0 4.13e-01 89.3% 38.1%
2566193 5058.1.1.1 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_1,MS_channel_1st 0.70 57.0 4.95e-01 88.0% 60.7%
3965862 5058.1.1.16 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_1 0.70 59.0 5.42e-01 93.3% 71.6%
3858695 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.70 51.0 4.91e-01 90.7% 68.2%
5012687 5058.1.1.16 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_1 0.69 59.0 5.45e-01 97.3% 72.6%
5034026 5058.1.1.16 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_1 0.69 59.0 5.23e-01 94.7% 65.7%
4931046 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 0.69 58.0 5.75e-01 93.3% 85.0%
3482882 5063.1.1.0 alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK 0.69 48.0 5.25e-01 78.7% 90.0%
4597483 5058.1.1.1 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_1,MS_channel_1st 0.69 58.0 4.92e-01 93.3% 56.7%
4982432 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 0.69 52.0 5.21e-01 96.0% 80.0%
3882597 4009.1.1.0 alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.68 50.0 4.79e-01 85.3% 66.7%
3436096 2004.1.1.364 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD+Helicase_C 0.68 56.0 3.37e-01 92.0% 31.2%
3966348 5058.1.1.16 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_1 0.68 56.0 5.43e-01 92.0% 80.0%
3385570 5043.1.1.21 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › DUF2393 0.67 51.0 5.16e-01 82.7% 84.0%
3269863 246.2.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.67 48.0 3.03e-01 78.7% 14.2%
3808722 633.6.1.2 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.65 53.0 4.17e-01 90.7% 68.1%
4930860 5058.1.1.16 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_1 0.64 53.0 5.04e-01 97.3% 75.6%
3607406 6026.1.1.0 alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.64 48.0 4.75e-01 81.3% 80.0%
4927047 632.19.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A 0.64 49.0 4.96e-01 89.3% 82.7%
3539738 10.12.1.1 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.63 44.0 3.16e-01 81.3% 24.0%
3503989 162.1.1.1 alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.61 44.0 4.09e-01 86.7% 60.0%
3331809 375.1.9.23 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › Sterile 0.61 50.0 3.79e-01 89.3% 56.6%
4947371 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.60 40.0 3.49e-01 70.7% 43.3%
4318142 230.3.1.1 a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.59 49.0 4.00e-01 90.7% 52.1%
3725613 101.1.6.0 alpha arrays › HTH › HTH › TrpR 0.51 43.0 3.92e-01 97.3% 95.2%