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SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00307

Bact-Vir

SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00307

Identity

Kingdom:
phage

Quality

76.5 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 15-69
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.66 48.0 3.70e-01 78.2% 46.7%
3bh1A03 3.40.140.40 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Domain of unknown function (DUF1846), C-terminal subdomain 0.65 44.0 3.31e-01 72.7% 72.6%
2n17A00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.64 43.0 4.36e-01 74.5% 69.6%
3deeA02 3.90.930.50 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.64 36.0 2.90e-01 100.0% 26.3%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 46.0 4.11e-01 78.2% 55.7%
4iauA01 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.62 39.0 3.52e-01 74.5% 43.6%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.62 44.0 3.62e-01 78.2% 56.0%
1y96A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.61 43.0 3.76e-01 74.5% 65.1%
1uvgA01 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.61 39.0 3.86e-01 74.5% 60.3%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.61 44.0 4.39e-01 94.5% 75.4%
2j4xA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.61 46.0 3.53e-01 89.1% 36.3%
3es1A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 38.0 3.02e-01 78.2% 28.6%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 42.0 3.55e-01 76.4% 49.0%
1wi0A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 44.0 3.59e-01 83.6% 48.7%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.59 41.0 4.03e-01 74.5% 67.2%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 38.0 3.18e-01 74.5% 34.6%
1u3eM02 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 0.59 44.0 4.16e-01 83.6% 79.4%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.58 42.0 3.31e-01 83.6% 42.3%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.58 41.0 3.27e-01 76.4% 70.1%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.58 44.0 3.05e-01 85.5% 98.5%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 41.0 3.66e-01 76.4% 53.8%
1o5uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.57 36.0 3.23e-01 72.7% 39.8%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.57 43.0 3.56e-01 85.5% 50.5%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.57 40.0 3.10e-01 76.4% 56.4%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.57 39.0 3.62e-01 72.7% 80.6%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 41.0 3.20e-01 80.0% 41.2%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.57 40.0 3.67e-01 76.4% 65.8%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 41.0 2.88e-01 80.0% 72.3%
2bvfA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.56 41.0 3.18e-01 83.6% 71.6%
2o2zA00 3.40.50.10680 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › CofD-like domains 0.56 42.0 2.74e-01 89.1% 83.5%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.55 44.0 2.69e-01 92.7% 13.1%
1hx6B01 2.70.9.30 Mainly Beta › Distorted Sandwich › Adenovirus Type 2 Hexon; domain 4 › Viral coat protein p3 0.55 39.0 2.66e-01 78.2% 44.6%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 40.0 3.01e-01 81.8% 43.4%
5escA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 40.0 3.21e-01 80.0% 48.7%
4dqnA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.55 44.0 3.32e-01 94.5% 84.2%
3fw8A02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.55 41.0 2.87e-01 83.6% 49.8%
3lgdA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.55 38.0 2.25e-01 74.5% 84.6%
1g25A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.55 38.0 3.72e-01 78.2% 72.3%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 43.0 3.17e-01 90.9% 33.1%
1mgpA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 42.0 3.17e-01 90.9% 33.5%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 39.0 3.07e-01 81.8% 45.9%
5ce8A01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.53 40.0 3.11e-01 81.8% 67.5%
2hhzA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 40.0 3.04e-01 81.8% 45.7%
2vfrA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.53 40.0 3.23e-01 89.1% 76.2%
2q18X01 3.10.330.40 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.52 35.0 3.30e-01 70.9% 98.6%
5jv4A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 38.0 2.94e-01 81.8% 53.5%
1dyoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 38.0 2.86e-01 81.8% 57.1%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.52 40.0 2.63e-01 89.1% 36.1%
3pjyA00 2.60.120.1140 Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF192 0.51 39.0 3.08e-01 94.5% 37.2%
7neaA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.50 38.0 3.16e-01 90.9% 97.5%
5bncB01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.50 37.0 2.86e-01 85.5% 42.3%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4988225 4187.1.1.2 ↗ a+b two layers › NosL/MerB-like › NosL/MerB-like › NosL/MerB-like › NosL 0.84 59.0 4.45e-01 74.5% 36.0%
3599295 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.72 55.0 3.42e-01 81.8% 40.7%
3692317 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.71 53.0 3.18e-01 81.8% 54.9%
4356442 887.1.1.1 ↗ a+b two layers › Ribosomal protein L30p/L7e › Ribosomal protein L30p/L7e › Ribosomal protein L30p/L7e › Ribosomal_L30 0.69 49.0 4.70e-01 76.4% 95.4%
4961835 377.9.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › HIT/MYND zinc finger-like › HIT/MYND zinc finger-like 0.67 46.0 4.29e-01 74.5% 60.3%
3415617 379.1.1.1 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_1 0.67 45.0 4.68e-01 74.5% 78.0%
3593442 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.66 48.0 3.91e-01 80.0% 41.0%
3804735 822.1.1.3 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF_ATXR3 0.66 46.0 4.54e-01 74.5% 69.5%
4001382 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 45.0 5.10e-01 74.5% 100.0%
3410496 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.66 43.0 4.57e-01 81.8% 79.2%
4075554 3019.1.1.0 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain 0.65 45.0 3.56e-01 74.5% 62.5%
4932504 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.64 43.0 3.70e-01 72.7% 41.1%
3476233 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.64 46.0 3.91e-01 89.1% 44.0%
3400250 379.1.1.3 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_2 0.64 43.0 4.47e-01 81.8% 78.0%
3486057 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.64 51.0 4.99e-01 90.9% 81.7%
4144066 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.64 43.0 3.67e-01 72.7% 43.3%
5025086 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.63 44.0 4.41e-01 72.7% 98.2%
3333626 822.1.1.0 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.63 44.0 4.31e-01 76.4% 68.3%
3400735 379.1.1.3 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_2 0.63 44.0 4.44e-01 81.8% 74.5%
4151528 1077.1.1.1 ↗ few secondary structure elements › RelA zinc-finger domain › RelA zinc-finger domain › RelA zinc-finger domain › RelA_RIS 0.62 42.0 4.24e-01 80.0% 70.9%
3617714 4357.1.1.1 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.61 44.0 4.08e-01 80.0% 94.7%
3629077 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.61 49.0 4.16e-01 90.9% 85.3%
3807153 221.1.1.88 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › CLU_N 0.61 42.0 3.55e-01 78.2% 41.0%
3941506 2002.1.1.16 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.61 51.0 3.19e-01 98.2% 20.6%
2856952 379.1.1.6 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › C6_KAZAL 0.61 42.0 3.78e-01 76.4% 50.6%
4295284 1077.1.1.1 ↗ few secondary structure elements › RelA zinc-finger domain › RelA zinc-finger domain › RelA zinc-finger domain › RelA_RIS 0.60 44.0 4.06e-01 98.2% 60.0%
4477814 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.60 39.0 3.37e-01 72.7% 40.0%
3925541 221.1.1.36 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N 0.60 42.0 3.24e-01 90.9% 31.5%
4268554 375.1.1.1 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › tRNA-synt_1 0.59 42.0 3.77e-01 76.4% 82.5%
4994 822.1.1.1 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.59 41.0 3.74e-01 74.5% 52.6%
4483288 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.59 40.0 3.42e-01 72.7% 60.0%
3581478 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.58 45.0 4.48e-01 96.4% 80.0%
4120000 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.58 43.0 3.39e-01 81.8% 94.4%
4342244 109.4.1.317 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Med5 0.57 39.0 2.82e-01 74.5% 30.0%
3022172 375.12.1.0 ↗ few secondary structure elements › Rubredoxin-like › Nicotinate phosphoribosyltransferase C-terminal domain-related › Nicotinate phosphoribosyltransferase C-terminal domain-related 0.56 34.0 3.28e-01 72.7% 50.8%
3469360 10.10.1.0 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) 0.55 39.0 3.56e-01 78.2% 77.5%
4976090 375.1.1.325 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › OapC 0.55 38.0 3.99e-01 80.0% 93.3%
3890381 4357.1.1.1 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.54 43.0 3.87e-01 90.9% 90.0%
4566976 375.14.2.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS2) 0.54 37.0 4.11e-01 89.1% 100.0%
2722401 4020.1.1.0 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes 0.54 43.0 3.20e-01 94.5% 82.5%
3685786 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 42.0 3.10e-01 100.0% 98.4%
3200355 72.1.1.0 ↗ beta sandwiches › gamma-Crystallin-like › gamma-Crystallin-like › gamma-Crystallin-like 0.52 38.0 3.30e-01 78.2% 48.9%
4958689 821.1.1.14 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF2797 0.52 43.0 4.20e-01 94.5% 91.7%
3991763 376.1.1.22 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4_3 0.52 34.0 3.69e-01 72.7% 97.5%
4662939 1077.1.1.1 ↗ few secondary structure elements › RelA zinc-finger domain › RelA zinc-finger domain › RelA zinc-finger domain › RelA_RIS 0.51 37.0 3.56e-01 89.1% 67.1%
1606334 4.10.1.0 ↗ beta barrels › SH3 › Fumarylacetoacetate hydrolase, FAH, N-terminal domain › Fumarylacetoacetate hydrolase, FAH, N-terminal domain 0.51 35.0 3.27e-01 72.7% 98.6%