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LSDeep1_scaffold_41_prodigal-single.1__X__X__00489

Bact-Vir

LSDeep1_scaffold_41_prodigal-single.1__X__X__00489

Identity

Kingdom:
phage

Quality

77.2 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 1-66_134-181
PDB
Domain cluster: representative
D2 medium residues 67-133
PDB
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e3vA03 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 0.75 44.0 4.75e-01 88.1% 69.6%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.73 46.0 4.22e-01 94.0% 50.0%
2a7oA00 1.10.1740.100 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Set2, Rpb1 interacting domain 0.73 60.0 5.19e-01 100.0% 59.0%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.69 44.0 3.99e-01 97.0% 48.9%
3s63A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.66 42.0 3.91e-01 86.6% 50.0%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 43.0 3.28e-01 74.6% 31.2%
1dosA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.63 52.0 3.34e-01 98.5% 17.9%
1rm6B02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.63 43.0 3.71e-01 86.6% 44.9%
1vx7301 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 46.0 4.48e-01 80.6% 70.3%
6pnjL00 1.20.1240.10 Mainly Alpha › Up-down Bundle › Photosystem 1 Reaction Centre Subunit Xi; Chain: L; › Photosystem I PsaL, reaction centre subunit XI 0.62 49.0 3.80e-01 98.5% 37.8%
3fhnA04 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.62 43.0 3.46e-01 82.1% 37.4%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 52.0 4.05e-01 91.0% 47.8%
2gxaE01 1.10.10.510 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Zinc finger, large T-antigen D1 domain 0.62 41.0 4.02e-01 92.5% 63.0%
6r8gB02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.61 44.0 3.22e-01 86.6% 29.4%
2w02B06 1.10.340.60 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › AcsD, palm domain, helix bundle 0.61 42.0 3.81e-01 100.0% 52.2%
2qg3A00 3.30.1960.10 Alpha Beta › 2-Layer Sandwich › SSo0622-like fold › tRNA wybutosine-synthesizing-like 0.61 49.0 3.51e-01 88.1% 84.0%
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.61 46.0 3.07e-01 80.6% 40.1%
2h8oA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.61 53.0 3.50e-01 100.0% 24.4%
1fkmA02 1.10.472.80 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Ypt/Rab-GAP domain of gyp1p, domain 3 0.61 51.0 4.11e-01 92.5% 97.7%
8b6jF01 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.60 49.0 4.95e-01 91.0% 95.5%
6opmD01 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.60 52.0 3.58e-01 100.0% 28.6%
5w8oA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 50.0 3.20e-01 95.5% 20.8%
4m52A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 51.0 3.56e-01 98.5% 42.8%
3fd0A01 3.90.1150.60 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Methioning gamme-lyase, C-terminal domain 0.58 49.0 3.57e-01 95.5% 45.1%
1wleA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.58 46.0 3.84e-01 85.1% 59.6%
1avoB00 1.20.120.180 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain 0.58 50.0 3.90e-01 94.0% 80.0%
7y11B01 1.10.8.20 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p 0.58 38.0 3.95e-01 89.6% 71.4%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 42.0 3.57e-01 80.6% 48.1%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.57 44.0 3.98e-01 85.1% 61.1%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.57 42.0 3.50e-01 79.1% 79.7%
3lomA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 50.0 3.29e-01 98.5% 92.7%
4ceiA03 6.10.250.2380 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 44.0 3.71e-01 83.6% 97.3%
1m6nA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.56 47.0 3.77e-01 94.0% 60.7%
3terA00 1.10.287.3550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 44.0 3.63e-01 85.1% 51.3%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.56 47.0 4.76e-01 97.0% 97.0%
4b1bA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 46.0 2.81e-01 98.5% 14.4%
1e6dM01 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.55 43.0 3.36e-01 85.1% 63.6%
1j3wC00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.54 41.0 3.34e-01 82.1% 96.2%
1s5jA04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.54 40.0 4.19e-01 98.5% 85.2%
2py5A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.54 45.0 3.33e-01 94.0% 98.9%
3if8B02 1.20.58.730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 43.0 3.87e-01 91.0% 81.0%
4ocqA01 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.53 46.0 3.15e-01 97.0% 43.8%
3vkgB06 1.20.920.20 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.53 47.0 3.15e-01 97.0% 47.3%
5ulcX00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 42.0 3.56e-01 92.5% 82.8%
3p0cA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 43.0 3.66e-01 91.0% 86.5%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.52 39.0 3.85e-01 83.6% 74.0%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.52 43.0 3.52e-01 100.0% 48.5%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4953551 4049.1.1.0 alpha superhelices › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like 0.70 49.0 5.03e-01 97.0% 76.9%
3306664 103.1.1.3 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › CRAL_TRIO_N 0.67 42.0 3.95e-01 82.1% 52.5%
5075473 241.6.1.2 a+b two layers › Type III secretory system chaperone-like › Arp2/3 complex subunits › Arp2/3 complex subunits › ARPC4 0.67 57.0 4.32e-01 95.5% 46.9%
4990692 7064.1.1.0 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 0.66 51.0 3.92e-01 100.0% 35.6%
3412240 174.1.1.33 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Erg28 0.66 46.0 3.67e-01 92.5% 37.7%
4984959 3758.1.1.113 alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › Rad50_zn_hook 0.64 48.0 3.08e-01 86.6% 16.4%
5014043 5051.1.1.0 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like 0.64 49.0 2.97e-01 82.1% 49.3%
3701383 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 47.0 3.38e-01 80.6% 29.7%
3756246 5086.1.1.117 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › WWC1 0.62 47.0 3.52e-01 80.6% 43.8%
3236134 4323.1.1.1 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 › V_ATPase_I 0.62 47.0 3.44e-01 80.6% 33.7%
4098211 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.61 46.0 4.16e-01 83.6% 60.0%
4092726 2003.1.2.8 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2,Pyr_redox_2 0.61 52.0 3.67e-01 98.5% 44.1%
4355829 206.1.2.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › SAICAR synthase › SAICAR_synt 0.60 46.0 3.03e-01 94.0% 19.0%
3788202 109.10.1.1 alpha superhelices › Repetitive alpha hairpins › Translin › Translin › Translin 0.60 47.0 3.13e-01 85.1% 22.4%
4592663 3978.1.1.1 alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › FA_desaturase 0.59 51.0 3.29e-01 100.0% 41.2%
4316900 3978.1.1.1 alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › FA_desaturase 0.59 51.0 3.33e-01 98.5% 33.2%
3516641 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.58 46.0 3.47e-01 85.1% 87.5%
3824673 2003.1.2.58 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox, Pyr_redox_2 0.58 52.0 3.24e-01 100.0% 21.1%
4307472 5057.1.1.1 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.58 51.0 3.81e-01 98.5% 78.2%
3962918 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 50.0 3.55e-01 98.5% 44.2%
5039562 633.22.1.16 alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › DUF1405 0.58 49.0 3.50e-01 94.0% 59.5%
5029889 5076.2.1.0 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ 0.58 47.0 3.12e-01 89.6% 39.6%
3958898 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 50.0 3.85e-01 98.5% 60.1%
4026070 5071.1.1.1 alpha bundles › cytochrome bc1 complex 11 kDa protein-like › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › UCR_hinge 0.58 50.0 4.99e-01 98.5% 95.6%
4682199 101.1.2.88 alpha arrays › HTH › HTH › winged helix domain › Dimerisation 0.58 43.0 3.34e-01 80.6% 36.0%
3924372 2004.5.1.8 a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain › C9orf72-like 0.57 46.0 3.17e-01 88.1% 65.7%
4016091 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 0.57 49.0 4.59e-01 98.5% 91.8%
3759004 622.1.1.22 alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › TF_AP-2 0.57 43.0 3.51e-01 80.6% 56.0%
3424878 5071.1.1.1 alpha bundles › cytochrome bc1 complex 11 kDa protein-like › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › UCR_hinge 0.57 46.0 4.57e-01 98.5% 88.4%
3615389 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.57 41.0 3.08e-01 79.1% 31.5%
3284147 150.5.1.52 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PE 0.56 43.0 3.69e-01 82.1% 52.4%
4929602 1079.1.1.0 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA 0.56 48.0 3.41e-01 97.0% 61.4%
3653773 605.1.1.231 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › PF28573 0.56 43.0 3.86e-01 85.1% 58.9%
3261925 3559.1.1.0 a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 0.56 42.0 3.15e-01 85.1% 34.2%
4983922 2007.1.2.13 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_6 0.56 46.0 3.11e-01 88.1% 66.4%
3291596 150.5.1.52 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PE 0.55 43.0 3.85e-01 86.6% 72.0%
4948812 2003.1.2.297 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_dim 0.55 47.0 2.94e-01 98.5% 17.9%
3469730 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.55 43.0 3.71e-01 85.1% 56.2%
3596488 3737.1.1.0 alpha duplicates or obligate multimers › Major allergen Bla g 1 tandem repeats › Major allergen Bla g 1 tandem repeats › Major allergen Bla g 1 tandem repeats 0.55 40.0 3.30e-01 85.1% 42.4%
4880327 3223.1.1.1 beta sandwiches › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › ASC 0.54 46.0 3.14e-01 97.0% 43.5%
3591905 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.54 40.0 3.35e-01 79.1% 49.6%
3877430 2004.1.1.19 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.53 45.0 3.01e-01 94.0% 77.5%
3663497 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.53 41.0 3.15e-01 85.1% 69.0%
3665032 2003.1.2.8 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2,Pyr_redox_2 0.53 44.0 3.12e-01 98.5% 29.4%
3627827 193.1.1.0 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like 0.52 47.0 3.98e-01 100.0% 81.8%
3199170 223.2.1.9 a+b three layers › Profilin-like › profilin-like › profilin-like › Sedlin_N 0.51 43.0 3.22e-01 92.5% 67.3%