←Back to structures

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00368

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00368

Identity

Kingdom:
phage

Quality

77.0 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 4-88
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1y8cA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.86 50.0 5.92e-01 77.6% 83.3%
3bxoA02 2.20.130.10 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › CAC2371-like domains 0.79 49.0 5.83e-01 76.5% 91.5%
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.78 48.0 5.52e-01 77.6% 84.1%
3fyfA00 2.40.128.410 Mainly Beta › Beta Barrel › Lipocalin › 0.77 52.0 4.27e-01 97.6% 39.6%
4c00A04 2.40.160.50 Mainly Beta › Beta Barrel › Porin › membrane protein fhac: a member of the omp85/tpsb transporter family 0.72 59.0 3.93e-01 98.8% 23.6%
3aa0B02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.68 63.0 5.08e-01 100.0% 61.3%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.67 56.0 4.88e-01 97.6% 61.5%
4afkA00 2.40.160.100 Mainly Beta › Beta Barrel › Porin › 0.67 59.0 3.67e-01 95.3% 34.0%
1aq3A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.66 53.0 4.56e-01 84.7% 60.5%
4akrA02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.66 62.0 5.02e-01 100.0% 59.9%
3fidA00 2.40.128.140 Mainly Beta › Beta Barrel › Lipocalin › Outer membrane protein 0.65 57.0 3.88e-01 95.3% 42.9%
1lshA01 2.30.230.10 Mainly Beta › Roll › Lipovitellin-phosvitin complex; beta-sheet shell regions › Lipovitellin; beta-sheet shell regions, chain A 0.65 58.0 4.09e-01 97.6% 36.9%
4ktpA01 2.70.98.40 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Glycoside hydrolase, family 65, N-terminal domain 0.65 59.0 4.13e-01 97.6% 58.4%
3gveA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.65 46.0 3.03e-01 74.1% 94.0%
3dcdA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.64 49.0 3.26e-01 80.0% 68.6%
1kyfA01 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.62 48.0 4.09e-01 81.2% 63.4%
4bboA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.62 50.0 4.57e-01 97.6% 65.5%
3qq2B00 2.40.128.130 Mainly Beta › Beta Barrel › Lipocalin › Autotransporter beta-domain 0.62 56.0 3.97e-01 100.0% 46.8%
4id2A00 2.40.128.510 Mainly Beta › Beta Barrel › Lipocalin › Protein of unknown function DUF4738 0.61 51.0 4.32e-01 89.4% 73.5%
4epaA00 2.40.170.20 Mainly Beta › Beta Barrel › Maltoporin; Chain A › TonB-dependent receptor, beta-barrel domain 0.61 53.0 3.19e-01 96.5% 13.9%
4kghA00 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.61 54.0 4.15e-01 98.8% 67.9%
4ojdH01 2.60.98.60 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Cell-cell fusogen EFF/AFF, domain 1 0.60 54.0 4.34e-01 100.0% 65.9%
6rtqA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.60 47.0 4.02e-01 97.6% 53.4%
1nqnA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.60 48.0 4.40e-01 100.0% 65.3%
1idpA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 49.0 4.15e-01 92.9% 78.9%
4r80A00 3.10.450.630 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 48.0 5.04e-01 95.3% 96.1%
3bghB01 3.30.160.180 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Putative neuraminyllactose-binding hemagglutinin homolog like domain 0.59 52.0 4.17e-01 100.0% 81.3%
4uv3E01 3.40.50.10610 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ABC-type transport auxiliary lipoprotein component 0.58 51.0 3.93e-01 100.0% 66.5%
7ufsA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.58 51.0 3.56e-01 96.5% 63.6%
4l8oA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 47.0 3.80e-01 89.4% 62.8%
1p4tA00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.57 49.0 4.14e-01 100.0% 56.1%
2ciuA00 3.10.450.320 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mitochondrial import inner membrane translocase subunit Tim21 0.57 48.0 4.27e-01 95.3% 64.2%
2e3nA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 46.0 3.41e-01 92.9% 42.0%
2obdA02 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.55 49.0 3.80e-01 100.0% 66.7%
2b1xB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 45.0 3.65e-01 91.8% 77.8%
2obdA01 3.15.20.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 2 › Bactericidal permeability-increasing protein; domain 2 0.54 47.0 3.35e-01 100.0% 37.1%
4xmeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 49.0 3.79e-01 100.0% 84.2%
5o46A00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 48.0 4.35e-01 98.8% 93.9%
4fumA01 2.20.230.10 Mainly Beta › Single Sheet › Resuscitation-promoting factor rpfb fold › Resuscitation-promoting factor rpfb. 0.53 37.0 3.95e-01 72.9% 93.2%
3q1nA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 46.0 3.15e-01 95.3% 72.1%
4b9gA00 2.60.40.3480 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 44.0 3.77e-01 95.3% 93.8%
4f8lA00 2.60.40.3590 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 42.0 3.61e-01 85.9% 79.7%
2nutB03 2.60.40.1670 Mainly Beta › Sandwich › Immunoglobulin-like › beta-sandwich domain of Sec23/24 0.53 37.0 3.13e-01 71.8% 62.4%
4lb8A02 2.60.40.3900 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 47.0 4.01e-01 100.0% 78.1%
3ejvA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 46.0 3.67e-01 94.1% 94.3%
3a76A01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 46.0 3.91e-01 97.6% 95.0%
3cjeA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 43.0 3.64e-01 94.1% 66.7%
5tseA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.51 45.0 3.90e-01 100.0% 75.7%
5azsA02 2.20.200.10 Mainly Beta › Single Sheet › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.51 38.0 3.88e-01 89.4% 80.7%
2p4bB02 3.30.200.100 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › MucB/RseB, C-terminal domain 0.51 42.0 4.05e-01 91.8% 78.6%
4lzkA00 2.60.40.3910 Mainly Beta › Sandwich › Immunoglobulin-like › Inclusion body protein 0.50 42.0 3.52e-01 96.5% 90.6%
3lohE05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 3.44e-01 84.7% 91.3%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3245468 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.83 46.0 4.06e-01 72.9% 39.2%
5021455 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.74 66.0 5.58e-01 100.0% 60.7%
3164538 5084.1.1.2 ↗ beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like › OmpA_membrane 0.69 62.0 4.73e-01 100.0% 54.9%
4066147 5084.5.1.11 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Porin_4 0.68 61.0 3.98e-01 96.5% 27.3%
4668983 4051.1.1.0 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz 0.67 60.0 4.80e-01 96.5% 53.8%
2658958 265.1.1.1 ↗ a+b two layers › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › Levi_coat 0.67 54.0 4.69e-01 97.6% 57.9%
4593791 5084.5.1.0 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin 0.67 62.0 4.00e-01 100.0% 37.2%
3840054 5084.1.1.15 ↗ beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like › HP_OMP 0.66 60.0 5.07e-01 100.0% 67.1%
4556738 7503.1.1.1 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › CsgG 0.65 53.0 3.78e-01 87.1% 34.4%
3598427 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.64 49.0 4.10e-01 82.4% 48.6%
3269001 12.3.1.46 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › ComC_SSD 0.64 58.0 4.09e-01 97.6% 75.9%
3827633 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.64 48.0 4.14e-01 78.8% 99.2%
4960625 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.64 50.0 3.95e-01 100.0% 40.0%
3459363 243.3.1.74 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF1668 0.63 49.0 4.97e-01 83.5% 87.1%
3784793 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 48.0 3.99e-01 81.2% 64.3%
4175473 5087.3.1.1 ↗ beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › Vit_open_b-sht 0.61 49.0 3.31e-01 87.1% 29.1%
4333087 5087.3.1.1 ↗ beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › Vit_open_b-sht 0.61 55.0 3.61e-01 98.8% 42.5%
4020277 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 47.0 3.60e-01 82.4% 72.8%
3192002 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.61 47.0 3.55e-01 82.4% 68.0%
3326287 4051.1.1.1 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.60 52.0 4.67e-01 95.3% 77.5%
1558627 243.1.1.15 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › T4BSS_DotI_IcmL 0.60 49.0 4.26e-01 91.8% 81.0%
3611830 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.60 52.0 3.29e-01 98.8% 60.0%
5034752 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.59 53.0 4.10e-01 100.0% 77.7%
4953123 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.58 52.0 3.26e-01 96.5% 35.3%
4984404 331.3.1.7 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › COXG 0.58 50.0 4.16e-01 95.3% 64.2%
4011378 63.1.1.0 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain 0.58 48.0 3.83e-01 91.8% 69.4%
3494118 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.57 50.0 4.10e-01 97.6% 59.5%
3737793 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.56 42.0 3.40e-01 82.4% 67.2%
3629462 5090.1.1.8 ↗ beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains › EFF-AFF 0.56 49.0 3.39e-01 97.6% 92.7%
5071365 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.55 46.0 2.98e-01 89.4% 75.6%
3385898 7503.1.1.1 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › CsgG 0.55 48.0 4.02e-01 100.0% 83.2%
3425035 243.1.1.122 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF28340 0.54 42.0 4.08e-01 85.9% 80.8%
3541003 243.3.1.1 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Cystatin 0.54 47.0 4.31e-01 94.1% 94.4%
3816972 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 44.0 3.55e-01 89.4% 63.6%
2712795 7503.1.1.20 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › DUF7499 0.54 46.0 3.76e-01 100.0% 84.3%
3856436 243.3.1.1 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Cystatin 0.54 47.0 4.33e-01 96.5% 94.5%
3791558 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.53 47.0 3.17e-01 97.6% 26.5%
220899 11.1.5.47 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › CssAB 0.53 44.0 3.77e-01 95.3% 93.8%
3917799 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 44.0 3.45e-01 100.0% 67.9%
5037531 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 45.0 2.67e-01 92.9% 14.3%
5054891 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.52 44.0 3.58e-01 100.0% 48.1%
3488078 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.52 39.0 2.82e-01 80.0% 55.1%
3388283 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.52 45.0 3.76e-01 100.0% 80.0%
3254691 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 41.0 3.73e-01 88.2% 75.8%
3552674 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.51 43.0 2.96e-01 91.8% 88.0%
3728831 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.51 42.0 3.60e-01 96.5% 92.9%
5010040 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.51 43.0 3.61e-01 100.0% 96.4%
3505139 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.51 43.0 2.92e-01 90.6% 85.2%
3574639 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.51 43.0 3.01e-01 94.1% 83.2%
5013600 512.1.1.2 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_2nd 0.51 43.0 3.77e-01 95.3% 63.8%