Back to structures

NC_028755.1__YP_009194828.1__CPT_Margaery13__00013

Bact-Vir

NC_028755.1__YP_009194828.1__CPT_Margaery13__00013

Identity

Accession:
NC_028755 ↗
Kingdom:
phage

Quality

92.0 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 3-72
PDB
Domain cluster: representative
CATH (55)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.79 52.0 5.34e-01 100.0% 71.2%
1cpqA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.77 69.0 5.62e-01 100.0% 86.8%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.77 69.0 5.69e-01 100.0% 83.2%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 52.0 4.64e-01 70.0% 91.7%
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.76 52.0 5.08e-01 100.0% 65.8%
1vb5A01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.75 63.0 5.75e-01 94.3% 76.6%
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.73 64.0 4.73e-01 94.3% 57.4%
2btqB03 1.10.287.600 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 50.0 5.65e-01 100.0% 94.3%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.73 49.0 4.89e-01 70.0% 91.9%
3dzaA01 1.20.120.1940 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YfdX protein domain 0.73 62.0 5.21e-01 94.3% 79.5%
1ug7A00 1.20.120.360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Axin interactor, dorsalization-associated protein, N-terminal domain 0.70 61.0 5.04e-01 98.6% 75.0%
1uujA00 1.20.960.30 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.70 40.0 3.96e-01 85.7% 52.6%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.70 47.0 4.16e-01 70.0% 82.4%
7qihA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.69 46.0 4.10e-01 70.0% 47.5%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.69 47.0 4.60e-01 71.4% 84.4%
3jz0A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.68 60.0 4.94e-01 100.0% 73.1%
1yo7A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.68 51.0 4.26e-01 80.0% 65.8%
2d2sA01 1.20.58.1210 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, N-terminal helical domain 0.67 45.0 3.87e-01 70.0% 51.7%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 46.0 4.24e-01 71.4% 94.6%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.65 45.0 4.04e-01 72.9% 81.6%
3kflA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.65 55.0 4.14e-01 94.3% 57.7%
4ewcA03 1.20.120.1660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.65 53.0 5.21e-01 95.7% 85.3%
2oebA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.65 56.0 4.43e-01 100.0% 75.0%
4kjmA02 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 0.65 44.0 4.84e-01 70.0% 96.4%
2yksA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.64 56.0 4.79e-01 100.0% 87.2%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.64 54.0 4.19e-01 94.3% 77.8%
3hqiA02 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.62 41.0 3.31e-01 74.3% 33.6%
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.62 43.0 3.96e-01 97.1% 56.2%
4akgA04 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.62 53.0 4.20e-01 100.0% 73.7%
2p0tA01 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.61 46.0 4.52e-01 94.3% 73.7%
4od4A01 1.10.357.140 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › UbiA prenyltransferase 0.61 50.0 4.00e-01 95.7% 73.1%
4fzlA01 1.10.150.790 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.61 50.0 4.76e-01 95.7% 82.8%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 40.0 4.21e-01 70.0% 92.1%
4nn1A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 43.0 3.14e-01 87.1% 27.3%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.58 51.0 4.03e-01 97.1% 63.7%
1vctA01 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 44.0 3.87e-01 82.9% 85.3%
1a22A00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 50.0 3.81e-01 100.0% 92.2%
6at7B03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.58 39.0 3.40e-01 100.0% 45.8%
4pfyA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.58 49.0 3.43e-01 95.7% 92.9%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.57 47.0 4.83e-01 100.0% 91.0%
1jetA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.57 47.0 3.46e-01 95.7% 94.9%
4ap2B01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.57 43.0 3.54e-01 81.4% 56.0%
3g0oA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 46.0 3.91e-01 100.0% 52.9%
2zxrA02 3.90.1640.30 Alpha Beta › Alpha-Beta Complex › inorganic pyrophosphatase (n-terminal core) › 0.57 46.0 3.41e-01 97.1% 72.6%
3s0aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.56 48.0 4.14e-01 100.0% 100.0%
1uqwA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.56 49.0 3.45e-01 97.1% 91.1%
2iylD01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.56 41.0 4.28e-01 88.6% 87.7%
2o7iA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.55 46.0 3.21e-01 95.7% 92.5%
2idgA00 1.10.3480.10 Mainly Alpha › Orthogonal Bundle › TorD-like › TorD-like 0.55 46.0 3.64e-01 98.6% 99.4%
2p0tA02 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.55 46.0 4.59e-01 97.1% 90.3%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 39.0 3.72e-01 78.6% 66.7%
1fkaG00 1.10.455.10 Mainly Alpha › Orthogonal Bundle › Ribosomal Protein S7 › Ribosomal protein S7/S5 0.54 40.0 3.39e-01 82.9% 63.3%
5cl3A00 1.25.10.90 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › 0.52 36.0 2.62e-01 74.3% 23.8%
3byiD00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.52 46.0 3.27e-01 100.0% 33.0%
2c12A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.51 41.0 3.51e-01 95.7% 55.9%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4244780 109.4.1.890 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C 0.87 59.0 3.83e-01 70.0% 18.9%
4025450 601.48.1.0 alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain 0.81 68.0 6.21e-01 91.4% 80.0%
3389963 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 0.80 49.0 5.00e-01 100.0% 62.9%
4962556 633.10.1.0 alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.80 52.0 4.30e-01 100.0% 40.9%
3484674 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.79 62.0 4.64e-01 91.4% 35.8%
4883406 622.4.1.1 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Blo-t-5 0.74 52.0 4.29e-01 100.0% 44.0%
4252460 2002.1.1.56 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Dus 0.74 63.0 4.08e-01 95.7% 22.5%
4888464 563.2.1.1 alpha bundles › ATPD N-terminal domain-like › Cas Cmr5-like › Cas Cmr5-like › Cas_Cmr5 0.74 67.0 5.15e-01 100.0% 78.9%
3693766 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.72 61.0 5.23e-01 95.7% 89.6%
5027248 7516.1.1.2 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.71 50.0 3.18e-01 74.3% 31.0%
3516214 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.70 47.0 4.40e-01 70.0% 85.6%
3969061 2002.1.1.56 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Dus 0.70 60.0 3.88e-01 95.7% 22.4%
4102269 604.34.1.1 alpha bundles › Spectrin repeat-like › Helical bundle domain in arginine decarboxylase › Helical bundle domain in arginine decarboxylase › Arg_decarb_HB 0.68 46.0 4.19e-01 70.0% 66.3%
3251843 601.1.2.5 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › TLN1-like_RS 0.68 58.0 4.16e-01 100.0% 44.1%
4370767 3104.1.1.1 alpha bundles › Putative ubiquinone biosynthesis protein › Putative ubiquinone biosynthesis protein › Putative ubiquinone biosynthesis protein › Coq4 0.67 46.0 3.23e-01 78.6% 22.7%
2972075 3759.1.1.1 alpha arrays › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antiterm 0.66 41.0 4.15e-01 97.1% 62.0%
3205500 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.65 54.0 3.84e-01 94.3% 35.1%
4016111 604.9.1.0 alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 0.65 45.0 4.43e-01 72.9% 82.7%
3434242 2003.1.5.31 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GRAS 0.64 55.0 3.39e-01 100.0% 90.4%
5072130 102.1.3.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain 0.64 56.0 4.76e-01 100.0% 81.7%
3221760 604.1.1.140 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF27005 0.64 44.0 4.18e-01 72.9% 94.1%
3378289 109.4.1.1262 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_long 0.64 45.0 3.53e-01 75.7% 36.1%
4953831 140.1.1.5 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon_1 0.64 55.0 4.05e-01 95.7% 55.0%
3984624 109.3.1.0 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.63 44.0 3.62e-01 74.3% 40.0%
4010197 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 45.0 3.36e-01 75.7% 28.6%
3383904 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 44.0 3.42e-01 75.7% 33.5%
3264196 5067.1.1.13 alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › ALMT 0.63 54.0 4.19e-01 100.0% 52.1%
3800855 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.62 55.0 4.35e-01 98.6% 61.4%
4956051 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.61 52.0 3.60e-01 95.7% 92.5%
3927665 192.29.1.118 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Tcp11 0.59 52.0 4.22e-01 100.0% 65.0%
3212799 632.1.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.59 45.0 4.23e-01 81.4% 97.6%
5079103 7523.1.1.0 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.58 46.0 3.68e-01 85.7% 43.6%
3677323 602.1.1.3 alpha arrays › L-aspartase middle domain-like › L-aspartase middle domain-like › L-aspartase middle domain-like › Lyase_aromatic 0.58 51.0 3.34e-01 100.0% 38.7%
3617250 109.27.1.0 alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.57 39.0 3.69e-01 74.3% 57.8%
5022564 1076.1.1.4 alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › PrsW-protease 0.54 46.0 3.47e-01 100.0% 90.5%
2581423 632.18.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.53 43.0 4.12e-01 97.1% 75.3%
4302483 3294.1.1.1 alpha complex topology › FAS type I helical domain › FAS type I helical domain › FAS type I helical domain › FAS_I_H 0.52 46.0 3.27e-01 97.1% 39.5%
3450460 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.51 44.0 4.41e-01 100.0% 95.7%
3785884 4966.1.1.1 alpha arrays › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase › RNA_pol 0.50 47.0 4.37e-01 100.0% 82.4%