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OP596613.1__WAX24318.1__X__00005

Bact-Vir

OP596613.1__WAX24318.1__X__00005

Identity

Accession:
OP596613 ↗
Kingdom:
phage

Quality

85.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bradyrhizobium_phage_ppBeUSDA76-1

TaxID: 3003363

Cluster

View cluster (9 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-87
PDB
Domain cluster: rep: EU849489.1__ACJ24752.1__X__00028__D18-95
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mgtA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.82 52.0 5.15e-01 72.9% 62.5%
4g6tA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.68 56.0 4.88e-01 89.4% 85.2%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.66 50.0 4.44e-01 82.4% 64.0%
4ebrA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.66 46.0 3.84e-01 74.1% 82.2%
3tqmA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.65 53.0 5.23e-01 88.2% 98.9%
3zm6A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.64 42.0 3.07e-01 84.7% 25.1%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 49.0 5.25e-01 87.1% 98.6%
2kouA00 3.30.160.380 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Dicer dimerisation domain 0.64 51.0 4.81e-01 92.9% 72.5%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.64 51.0 5.05e-01 85.9% 100.0%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 49.0 5.14e-01 92.9% 92.3%
4dm5A00 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.62 41.0 4.09e-01 71.8% 65.5%
1dxkA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.62 45.0 3.36e-01 77.6% 95.0%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.60 45.0 4.80e-01 82.4% 93.1%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 45.0 3.72e-01 78.8% 64.4%
2aehA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 40.0 3.65e-01 71.8% 52.3%
3a32A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.60 47.0 4.05e-01 87.1% 83.0%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.59 44.0 3.80e-01 81.2% 70.0%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.59 52.0 4.58e-01 100.0% 81.7%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 43.0 4.68e-01 81.2% 98.5%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.58 41.0 4.09e-01 72.9% 70.8%
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.58 50.0 4.72e-01 100.0% 95.3%
2v14A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.57 50.0 4.39e-01 100.0% 88.1%
1xteA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.57 49.0 4.53e-01 100.0% 86.2%
2gfgA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.57 47.0 3.61e-01 90.6% 78.0%
2ar5A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.56 49.0 4.45e-01 100.0% 91.5%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.56 38.0 3.30e-01 70.6% 67.6%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.54 31.0 2.90e-01 77.6% 45.6%
3thxA02 3.30.420.110 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › MutS, connector domain 0.52 39.0 3.20e-01 81.2% 88.5%
2zgoA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 43.0 3.49e-01 90.6% 65.9%
1ul7A00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.51 35.0 3.37e-01 70.6% 63.7%
3q63F00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 39.0 3.39e-01 83.5% 61.9%
3cgbA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.50 36.0 3.40e-01 76.5% 79.1%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4021911 7504.1.1.5 ↗ a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › DUF5427 0.67 52.0 4.16e-01 84.7% 96.0%
3241869 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.65 53.0 4.91e-01 89.4% 69.1%
4801232 216.1.1.5 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › BRE 0.65 52.0 4.58e-01 89.4% 81.5%
5061259 330.2.1.1 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.65 53.0 5.04e-01 89.4% 99.0%
4043415 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.65 49.0 3.10e-01 87.1% 15.2%
4058654 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.65 52.0 5.03e-01 90.6% 91.9%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 47.0 4.61e-01 83.5% 72.2%
3780194 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 49.0 3.54e-01 87.1% 28.6%
3515207 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 49.0 4.85e-01 87.1% 77.8%
4036906 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.64 50.0 5.12e-01 85.9% 100.0%
5810 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 49.0 4.71e-01 88.2% 71.7%
3987293 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.63 41.0 3.07e-01 84.7% 25.5%
5052825 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.63 48.0 4.53e-01 82.4% 84.8%
3226497 145.1.1.1 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box 0.62 45.0 4.13e-01 77.6% 57.4%
3802643 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.62 46.0 4.47e-01 87.1% 71.6%
3439202 220.1.1.30 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BEACH 0.62 43.0 4.31e-01 71.8% 71.8%
3246050 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.62 45.0 4.43e-01 83.5% 72.2%
4090939 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.62 49.0 5.00e-01 87.1% 95.0%
3718216 4051.1.1.0 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz 0.62 45.0 4.07e-01 80.0% 97.6%
4040973 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.61 46.0 4.91e-01 84.7% 97.1%
5003966 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.61 42.0 4.75e-01 71.8% 95.4%
3585171 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.61 46.0 4.63e-01 83.5% 80.0%
3619264 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.61 51.0 5.06e-01 96.5% 86.7%
3797649 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 47.0 4.36e-01 83.5% 70.9%
4027910 2485.1.1.1 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.60 46.0 3.93e-01 83.5% 83.6%
3982054 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.59 44.0 3.42e-01 78.8% 56.3%
3789856 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.59 49.0 4.44e-01 91.8% 80.0%
1296460 216.2.1.1 ↗ a+b two layers › UBC-like › Thermo-DBP-RP2 C-terminal domain › Thermo-DBP-RP2 C-terminal domain › Thermo-DBP 0.59 52.0 4.85e-01 100.0% 80.2%
4040354 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.58 44.0 4.58e-01 83.5% 92.0%
3693249 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 50.0 4.42e-01 100.0% 83.8%
3580295 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 0.57 41.0 3.24e-01 75.3% 77.1%
4984607 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.56 38.0 3.72e-01 70.6% 67.4%
3196947 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 41.0 2.45e-01 78.8% 38.9%
3967506 300.1.1.8 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc_2 0.53 37.0 2.74e-01 74.1% 71.2%
3338126 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.51 37.0 2.68e-01 77.6% 78.8%
3289254 220.1.1.82 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_6 0.50 34.0 3.35e-01 78.8% 63.2%