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LSDeep1_scaffold_42_prodigal-single.1__X__X__00196

Bact-Vir

LSDeep1_scaffold_42_prodigal-single.1__X__X__00196

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 7-59
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cobA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.72 52.0 5.60e-01 84.9% 93.2%
3h5tA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.64 42.0 4.47e-01 90.6% 76.6%
1t3dA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.63 53.0 3.94e-01 96.2% 61.4%
6xssA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 45.0 4.16e-01 79.2% 59.4%
1bqbA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.62 55.0 3.95e-01 96.2% 41.0%
2w7nA00 1.10.10.2690 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.61 47.0 3.98e-01 94.3% 48.9%
1rr7A02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.59 46.0 4.85e-01 86.8% 95.8%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.58 49.0 4.38e-01 100.0% 71.6%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.57 46.0 3.63e-01 96.2% 55.6%
4ar9A02 1.10.390.20 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › 0.56 41.0 3.11e-01 84.9% 31.0%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 39.0 3.10e-01 81.1% 62.5%
4rg6A02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 40.0 3.63e-01 83.0% 58.4%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 37.0 3.50e-01 79.2% 80.0%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 39.0 3.17e-01 83.0% 86.1%
3t0yA02 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 0.51 36.0 3.58e-01 92.5% 71.7%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4336911 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.71 56.0 5.18e-01 90.6% 67.1%
5068347 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.68 59.0 4.15e-01 100.0% 42.9%
3870636 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.62 44.0 4.20e-01 77.4% 86.2%
5025549 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 44.0 4.27e-01 90.6% 78.5%
5025960 101.1.1.558 alpha arrays › HTH › HTH › Three-helical HTH › DUF7523 0.54 44.0 4.38e-01 96.2% 92.7%
D2 medium residues 60-226_294-325
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF26125.1 best AcrVA2-like 41.0 3.60e-10 84.9% 60.0%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3n8bA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 25.0 4.01e-01 89.4% 97.3%
1c6rA00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.54 26.0 3.69e-01 74.4% 100.0%
2gtlN02 2.40.128.620 Mainly Beta › Beta Barrel › Lipocalin › 0.51 36.0 3.86e-01 71.9% 82.4%
4emoC00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 30.0 3.69e-01 76.9% 97.4%
5e4bA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.50 37.0 3.88e-01 81.9% 84.7%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4027513 331.9.1.0 a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.65 30.0 3.88e-01 80.9% 73.9%
5036533 3435.1.1.0 a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.61 36.0 3.47e-01 81.9% 49.8%
5043905 3435.1.1.0 a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.58 34.0 3.31e-01 81.4% 50.2%
3651259 4001.1.1.4 a+b duplicates or obligate multimers › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › Cullin_AB 0.57 22.0 3.14e-01 78.9% 72.6%
3380843 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.52 35.0 3.81e-01 84.4% 80.6%
3823244 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.51 31.0 3.71e-01 76.9% 89.6%
D3 medium residues 228-280
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.80 67.0 6.41e-01 90.6% 95.0%
1jadA00 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.78 62.0 3.98e-01 86.8% 63.6%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.77 56.0 3.83e-01 77.4% 84.2%
2fonA04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.77 65.0 4.96e-01 98.1% 60.5%
5mmjo00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.77 63.0 5.56e-01 88.7% 76.0%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.76 61.0 5.77e-01 86.8% 92.1%
4a4kA01 1.20.1500.20 Mainly Alpha › Up-down Bundle › YheA-like fold › 0.75 66.0 5.03e-01 94.3% 48.7%
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 0.75 62.0 6.46e-01 88.7% 100.0%
4qmaA01 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.75 52.0 5.64e-01 75.5% 100.0%
1l5jA03 3.40.1060.10 Alpha Beta › 3-Layer(aba) Sandwich › Aconitase; Domain 2 › Aconitase, Domain 2 0.75 57.0 3.92e-01 81.1% 41.6%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.74 65.0 5.84e-01 100.0% 73.0%
4g3vA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.74 55.0 3.90e-01 81.1% 88.3%
2v6eA01 1.10.287.3180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 57.0 5.15e-01 86.8% 86.7%
3sllA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.73 54.0 5.19e-01 81.1% 93.4%
3f0cA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.73 59.0 4.29e-01 88.7% 42.4%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.73 58.0 4.38e-01 90.6% 78.2%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.72 56.0 4.90e-01 86.8% 57.3%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 60.0 5.50e-01 94.3% 80.3%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.72 59.0 5.67e-01 94.3% 88.9%
3lwjA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.72 60.0 4.05e-01 92.5% 38.3%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.71 57.0 4.68e-01 86.8% 49.5%
7tzoA01 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.71 60.0 4.15e-01 94.3% 60.9%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.71 58.0 4.98e-01 92.5% 67.1%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.70 57.0 4.36e-01 92.5% 78.6%
1kmiZ02 1.10.287.500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 59.0 4.48e-01 100.0% 54.5%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.67 55.0 4.32e-01 94.3% 52.1%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.66 49.0 4.43e-01 79.2% 59.7%
1zylA03 1.20.1270.170 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.66 53.0 4.32e-01 90.6% 57.3%
2lseA00 1.20.120.1360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.66 46.0 3.91e-01 83.0% 41.6%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.65 50.0 4.80e-01 90.6% 93.8%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.65 55.0 4.51e-01 98.1% 63.7%
3w8hB00 1.10.12.70 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › 0.65 47.0 4.49e-01 81.1% 68.2%
1oisA01 1.10.10.41 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Yeast DNA topoisomerase - domain 1 0.65 47.0 4.01e-01 81.1% 48.9%
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 44.0 4.04e-01 79.2% 55.9%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.63 50.0 4.81e-01 96.2% 93.8%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.61 47.0 4.47e-01 92.5% 77.1%
1f14A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 46.0 3.29e-01 92.5% 50.0%
8d8lN01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 45.0 4.03e-01 94.3% 69.8%
1cbyA00 3.40.198.10 Alpha Beta › 3-Layer(aba) Sandwich › Delta-endotoxin CytB › Delta-endotoxin CytB-like 0.50 38.0 2.64e-01 90.6% 78.9%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5030302 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 0.88 79.0 6.33e-01 96.2% 62.1%
3576047 3652.1.1.0 alpha duplicates or obligate multimers › Qua1 › Qua1 › Qua1 0.79 63.0 6.54e-01 84.9% 90.0%
2055367 650.1.1.3 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › HsbA 0.79 67.0 6.11e-01 94.3% 85.7%
3215346 397.7.1.0 few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.79 62.0 6.43e-01 86.8% 98.0%
4203104 3560.1.1.7 a+b complex topology › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Med10 0.78 68.0 4.95e-01 98.1% 44.1%
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 0.77 66.0 4.11e-01 96.2% 19.7%
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 0.77 63.0 6.41e-01 92.5% 100.0%
4101335 2006.1.4.8 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN_5 0.76 64.0 4.12e-01 90.6% 23.6%
3967173 7542.1.2.1 a/b three-layered sandwiches › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain II › Aconitase 0.74 57.0 4.04e-01 81.1% 48.0%
4132296 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 0.74 63.0 6.07e-01 96.2% 95.0%
3242821 192.10.1.0 alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain 0.74 57.0 5.51e-01 86.8% 80.0%
223791 186.1.1.9 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › TelK_N 0.73 57.0 5.10e-01 86.8% 84.4%
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 0.73 61.0 5.76e-01 94.3% 80.0%
3579325 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.73 56.0 4.48e-01 84.9% 41.9%
3311170 208.1.1.0 beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes 0.71 58.0 3.92e-01 92.5% 25.7%
3793084 192.29.1.234 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › PF27984 0.71 60.0 4.43e-01 100.0% 38.7%
4971099 4044.1.1.0 alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins 0.70 57.0 4.80e-01 90.6% 55.6%
3281127 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.70 59.0 5.05e-01 100.0% 70.0%
3413073 138.1.1.0 alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.69 54.0 4.16e-01 86.8% 39.2%
3575797 904.1.1.28 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain › PF27984 0.69 57.0 3.94e-01 96.2% 30.3%
3331809 375.1.9.23 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › Sterile 0.69 59.0 4.14e-01 98.1% 34.3%
3619877 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.68 57.0 4.53e-01 96.2% 51.3%
5033258 5045.1.1.0 alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A 0.67 57.0 3.71e-01 100.0% 25.1%
3566627 604.1.1.247 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF846 0.67 51.0 4.29e-01 88.7% 56.0%
3491670 614.1.1.0 alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.65 55.0 5.47e-01 98.1% 100.0%
4682722 237.1.1.5 a+b complex topology › ADP-ribosylation › ADP-ribosylation › ADP-ribosylation › RolB_RolC 0.61 50.0 3.41e-01 90.6% 33.5%