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js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00120

Bact-Vir

js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00120

Identity

Kingdom:
phage

Quality

78.0 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 1-52
PDB
Domain cluster: representative
CATH (59)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.91 83.0 7.50e-01 100.0% 78.3%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 84.0 7.78e-01 100.0% 93.7%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 83.0 7.76e-01 100.0% 100.0%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.90 78.0 6.07e-01 100.0% 46.2%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.90 82.0 7.32e-01 100.0% 78.9%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.90 82.0 6.84e-01 100.0% 65.1%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.89 75.0 7.65e-01 90.4% 96.1%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.89 80.0 7.36e-01 100.0% 92.5%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.88 80.0 6.17e-01 100.0% 50.9%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.88 79.0 5.43e-01 100.0% 33.3%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.88 78.0 6.65e-01 98.1% 67.9%
2wmmA01 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 0.88 70.0 7.23e-01 86.5% 100.0%
7metA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.87 79.0 4.79e-01 100.0% 17.8%
1yxrA01 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 79.0 6.94e-01 100.0% 70.3%
5ux1D00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 78.0 5.15e-01 100.0% 26.4%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.87 79.0 7.33e-01 100.0% 81.2%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.87 79.0 6.58e-01 100.0% 60.5%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 76.0 5.08e-01 100.0% 26.3%
4jvyB00 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.86 65.0 4.29e-01 100.0% 22.1%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.86 78.0 4.54e-01 100.0% 13.6%
1vs5O00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.85 71.0 5.95e-01 100.0% 54.5%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.85 76.0 7.39e-01 100.0% 89.7%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.85 75.0 7.09e-01 96.2% 100.0%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.85 75.0 6.50e-01 100.0% 69.1%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.85 75.0 7.04e-01 100.0% 82.8%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.85 71.0 5.08e-01 100.0% 33.1%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.85 69.0 6.56e-01 88.5% 100.0%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.85 72.0 4.67e-01 96.2% 23.4%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.84 72.0 6.95e-01 100.0% 84.5%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 70.0 6.21e-01 100.0% 64.0%
1qgtB00 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.83 74.0 5.35e-01 100.0% 42.0%
1wpbG01 1.10.287.680 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.83 56.0 5.59e-01 76.9% 68.5%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 72.0 6.39e-01 100.0% 72.4%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.82 72.0 6.93e-01 98.1% 100.0%
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 0.82 73.0 4.65e-01 100.0% 21.2%
1ucuA01 6.10.280.190 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 72.0 6.58e-01 100.0% 92.6%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.81 68.0 5.80e-01 94.2% 78.8%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.79 72.0 6.70e-01 100.0% 87.3%
3pt1A02 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.78 70.0 5.27e-01 100.0% 67.5%
3zdmB00 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 0.76 59.0 6.01e-01 88.5% 90.0%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 68.0 6.00e-01 100.0% 71.6%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.75 63.0 5.38e-01 100.0% 70.0%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 58.0 5.85e-01 86.5% 86.8%
4asvA00 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 0.74 56.0 4.97e-01 84.6% 57.0%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.74 60.0 5.11e-01 98.1% 100.0%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.74 65.0 5.07e-01 100.0% 46.8%
2dw4A03 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.72 60.0 4.96e-01 100.0% 50.5%
4cpgA00 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 0.72 56.0 5.18e-01 88.5% 66.7%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 63.0 5.79e-01 100.0% 77.6%
4dnnA00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 58.0 5.89e-01 98.1% 100.0%
4cb8A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.69 60.0 3.47e-01 100.0% 12.7%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 51.0 4.81e-01 90.4% 69.1%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.67 61.0 5.10e-01 100.0% 62.4%
2vkzA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.67 61.0 3.81e-01 100.0% 20.2%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.66 47.0 4.40e-01 100.0% 59.2%
4qxbB00 6.10.280.250 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 59.0 5.37e-01 100.0% 76.5%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.64 52.0 5.11e-01 100.0% 88.1%
3lwjA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.63 55.0 3.74e-01 100.0% 30.1%
2yfqB01 1.10.8.1210 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.59 44.0 4.40e-01 80.8% 78.8%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030332 604.7.1.0 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.95 89.0 5.38e-01 100.0% 18.2%
3623143 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.93 86.0 7.15e-01 100.0% 61.2%
3191420 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.93 86.0 7.91e-01 100.0% 84.6%
2570270 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.92 75.0 7.59e-01 86.5% 100.0%
4196271 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.92 85.0 4.93e-01 100.0% 13.5%
3593736 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.92 85.0 6.67e-01 100.0% 73.0%
4927769 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 0.92 85.0 6.82e-01 100.0% 55.9%
3253283 192.5.1.14 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.92 84.0 6.75e-01 100.0% 54.7%
4228031 109.4.1.128 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G_like_2 0.91 84.0 5.11e-01 100.0% 18.1%
4937739 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.91 83.0 5.97e-01 100.0% 54.1%
5078221 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.90 83.0 5.84e-01 100.0% 35.9%
4349607 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.90 83.0 6.35e-01 100.0% 47.3%
3795985 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.90 81.0 6.75e-01 98.1% 60.0%
3721468 604.7.1.5 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › RMP1 0.90 82.0 6.05e-01 100.0% 41.6%
4042007 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.89 82.0 6.25e-01 100.0% 47.3%
4645372 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 0.89 81.0 6.50e-01 100.0% 54.7%
3497897 3939.1.1.0 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.88 82.0 7.29e-01 100.0% 74.3%
3475201 3652.1.1.2 ↗ alpha duplicates or obligate multimers › Qua1 › Qua1 › Qua1 › STAR_dimer 0.88 67.0 6.37e-01 100.0% 70.0%
3415405 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 0.88 81.0 4.63e-01 100.0% 11.7%
5016147 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 0.87 79.0 5.70e-01 100.0% 38.5%
4385544 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 80.0 6.97e-01 100.0% 78.7%
3382780 2006.1.1.8 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › 5_nucleotid 0.87 78.0 4.62e-01 100.0% 14.9%
2456957 192.13.1.1 ↗ alpha bundles › Long alpha-hairpin › ISY1 N-terminal domain-like › ISY1 N-terminal domain-like › Isy1 0.87 78.0 7.66e-01 100.0% 92.9%
3970127 150.1.2.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase 0.86 75.0 5.01e-01 100.0% 26.0%
3988020 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 0.85 77.0 7.14e-01 100.0% 83.1%
5006936 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 0.85 70.0 6.58e-01 100.0% 75.4%
4801882 192.1.1.1 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › MCPsignal 0.84 73.0 6.89e-01 100.0% 98.4%
3269731 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.81 63.0 4.85e-01 84.6% 66.1%
3274546 7516.1.1.79 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glyco_trans_2_3 0.81 70.0 3.94e-01 100.0% 9.7%
3171326 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.79 70.0 5.77e-01 100.0% 57.9%
3858340 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.79 66.0 4.68e-01 88.5% 96.4%
4030667 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.79 69.0 5.82e-01 100.0% 57.8%
4992578 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.77 69.0 5.64e-01 100.0% 68.4%
3691039 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 68.0 5.93e-01 100.0% 68.8%
4010384 361.1.1.0 ↗ few secondary structure elements › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain 0.77 65.0 6.16e-01 100.0% 86.2%
3281235 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.75 63.0 5.73e-01 100.0% 70.7%
4527465 101.1.4.83 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › Med10 0.75 60.0 4.76e-01 96.2% 41.7%
3941960 5086.1.1.86 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_YBHG 0.74 62.0 4.76e-01 100.0% 40.8%
3725377 192.15.1.44 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.73 61.0 5.22e-01 100.0% 60.0%
2914508 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.70 55.0 3.53e-01 96.2% 16.9%
3355246 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.70 58.0 5.08e-01 92.3% 93.8%
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 0.67 55.0 3.37e-01 100.0% 14.1%