←Back to structures

rifoxyd1_full_scaffold_5_prodigal-single.1__X__X__00133

Bact-Vir

rifoxyd1_full_scaffold_5_prodigal-single.1__X__X__00133

Identity

Kingdom:
phage

Quality

87.0 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 3-53
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.81 70.0 6.55e-01 100.0% 77.8%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.73 64.0 5.66e-01 100.0% 72.4%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.70 55.0 5.10e-01 100.0% 68.2%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 58.0 4.64e-01 100.0% 100.0%
2eddA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 53.0 4.17e-01 100.0% 38.4%
7y8sB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 54.0 4.63e-01 100.0% 51.7%
3lb6C01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 50.0 4.21e-01 100.0% 45.5%
1uc6A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 51.0 4.07e-01 100.0% 38.5%
1tdqA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 55.0 4.57e-01 100.0% 51.1%
4lsdF00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 52.0 4.28e-01 100.0% 44.9%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.66 57.0 5.25e-01 100.0% 79.1%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 54.0 4.36e-01 100.0% 47.5%
3g7mA00 2.60.110.10 Mainly Beta › Sandwich › Thaumatin › Thaumatin 0.64 47.0 3.41e-01 100.0% 27.2%
2v5yA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 44.0 3.66e-01 100.0% 38.9%
6kwzA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 47.0 3.85e-01 100.0% 42.9%
2j3wC00 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.63 42.0 3.10e-01 76.5% 25.9%
8gk4C02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.62 54.0 4.44e-01 100.0% 100.0%
2llzA01 3.30.70.2360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 52.0 4.46e-01 100.0% 88.9%
2pjyC00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.62 53.0 4.67e-01 100.0% 64.6%
3r5lA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.62 54.0 4.17e-01 100.0% 49.1%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.61 52.0 3.71e-01 100.0% 31.1%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 44.0 3.40e-01 100.0% 31.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.61 51.0 4.07e-01 100.0% 46.8%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.60 49.0 3.57e-01 100.0% 38.4%
2oo3A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 49.0 3.22e-01 100.0% 21.0%
6kryA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.60 48.0 3.74e-01 100.0% 73.2%
1mt1B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.60 49.0 3.97e-01 100.0% 52.7%
5z0uA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 50.0 3.82e-01 100.0% 40.3%
2b39A10 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.58 45.0 3.52e-01 100.0% 37.9%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.58 49.0 4.15e-01 100.0% 56.5%
2n1kA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 42.0 3.50e-01 100.0% 40.6%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.57 48.0 4.02e-01 100.0% 58.2%
4eq3A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 44.0 3.62e-01 100.0% 44.4%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 47.0 4.13e-01 100.0% 94.0%
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.55 44.0 3.73e-01 100.0% 89.2%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.55 47.0 2.94e-01 100.0% 21.1%
2vfkA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.55 45.0 3.08e-01 96.1% 88.8%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 40.0 3.36e-01 100.0% 41.7%
5utkA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 41.0 3.63e-01 100.0% 53.0%
4me3A03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.54 46.0 4.54e-01 100.0% 96.4%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 44.0 3.54e-01 100.0% 49.6%
3hlbD00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 40.0 2.43e-01 86.3% 48.3%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 44.0 3.75e-01 100.0% 57.4%
4avrA00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.53 46.0 3.77e-01 98.0% 59.6%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 38.0 3.39e-01 100.0% 50.0%
2avxA00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 40.0 2.90e-01 88.2% 82.5%
5lvxC02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 42.0 3.47e-01 100.0% 98.1%
3lsoA01 2.60.40.2270 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 37.0 2.65e-01 78.4% 36.9%
2qlvB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 39.0 3.45e-01 98.0% 54.0%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.84 68.0 6.92e-01 100.0% 90.0%
5074648 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.79 72.0 6.28e-01 100.0% 73.3%
5000510 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 73.0 6.33e-01 100.0% 72.0%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 72.0 6.85e-01 100.0% 93.2%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.79 72.0 5.59e-01 100.0% 52.4%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 71.0 6.69e-01 100.0% 91.7%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 71.0 6.58e-01 100.0% 87.3%
4160542 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 70.0 6.74e-01 100.0% 94.8%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.78 71.0 6.31e-01 100.0% 78.6%
3668699 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.78 70.0 5.99e-01 100.0% 65.0%
5012895 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.78 71.0 6.93e-01 100.0% 96.4%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.77 70.0 6.46e-01 100.0% 85.9%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.77 70.0 6.71e-01 100.0% 94.8%
2831852 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.77 69.0 5.45e-01 100.0% 54.5%
5015713 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.76 69.0 6.55e-01 100.0% 96.7%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.76 68.0 5.95e-01 100.0% 73.3%
3396683 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.74 63.0 5.47e-01 100.0% 62.0%
4962335 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.72 61.0 5.66e-01 100.0% 75.4%
5014684 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.71 63.0 6.07e-01 100.0% 89.7%
4930766 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.67 56.0 4.16e-01 100.0% 36.3%
4152762 2492.1.1.20 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › APOBEC3 0.65 54.0 3.76e-01 100.0% 27.4%
3256398 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 57.0 4.62e-01 100.0% 53.7%
3269973 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.64 56.0 4.57e-01 100.0% 96.8%
4974427 304.5.1.1 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.63 55.0 4.89e-01 100.0% 100.0%
4265395 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.62 52.0 4.14e-01 100.0% 44.3%
3210904 12.6.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycoside hydrolase family 127 middle domain-related › Glycoside hydrolase family 127 middle domain-related 0.62 53.0 4.00e-01 100.0% 37.8%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.62 53.0 5.37e-01 98.0% 100.0%
3932964 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.61 53.0 3.46e-01 100.0% 91.9%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.61 50.0 3.77e-01 100.0% 35.0%
4948793 304.134.1.3 ↗ a+b two layers › Alpha-beta plaits › MJ1480-like › MJ1480-like › PF26798 0.61 53.0 4.60e-01 100.0% 100.0%
3789334 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.60 50.0 4.05e-01 100.0% 46.7%
3963369 4222.1.1.2 ↗ a+b two layers › ImmE5-like › ImmE5-like › ImmE5-like › Imm40 0.60 48.0 4.14e-01 100.0% 55.8%
3941935 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.60 49.0 3.95e-01 100.0% 45.2%
3453549 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 48.0 3.75e-01 100.0% 40.9%
3955667 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.59 47.0 3.84e-01 100.0% 45.7%
3405278 382.1.1.3 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Activin_recp 0.58 50.0 4.08e-01 100.0% 55.0%
4979407 5103.1.1.0 ↗ a/b three-layered sandwiches › Insert domain in hypothetical protein PF0380 › Insert domain in hypothetical protein PF0380 › Insert domain in hypothetical protein PF0380 0.58 44.0 3.60e-01 88.2% 60.0%
3286547 223.3.1.0 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins 0.58 44.0 3.20e-01 86.3% 82.5%
3414928 382.1.1.6 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › QVR 0.58 46.0 4.09e-01 100.0% 60.2%
3738589 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.57 47.0 3.90e-01 100.0% 48.6%
4927303 525.1.1.1 ↗ a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.57 50.0 3.82e-01 100.0% 84.2%
3603767 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.57 48.0 3.90e-01 100.0% 48.6%
4028150 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.57 49.0 3.86e-01 100.0% 50.0%
4969338 212.1.1.12 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › UPF0029 0.56 39.0 3.03e-01 78.4% 31.2%
3744530 302.4.1.1 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.55 45.0 3.70e-01 100.0% 47.3%
4155354 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.55 44.0 3.59e-01 100.0% 44.2%
5018298 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.55 46.0 3.69e-01 100.0% 44.3%
3533360 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 43.0 3.56e-01 100.0% 46.4%
4175825 387.1.1.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.53 47.0 4.30e-01 100.0% 75.4%
3935404 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.53 44.0 3.77e-01 96.1% 95.6%
5055086 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.53 45.0 3.74e-01 98.0% 73.7%
3599827 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 42.0 3.14e-01 100.0% 37.7%
3939823 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 44.0 3.18e-01 100.0% 33.3%
3574971 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.52 40.0 4.09e-01 100.0% 88.0%
3999847 2007.2.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II 0.52 43.0 3.07e-01 96.1% 45.1%
3392943 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 41.0 3.17e-01 100.0% 37.2%
3262497 11.1.1.801 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7035 0.51 41.0 3.20e-01 100.0% 41.5%
3186365 217.1.1.2 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_4 0.50 42.0 2.84e-01 98.0% 37.1%