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OP596615.1__WAX24474.1__X__00032

Bact-Vir

OP596615.1__WAX24474.1__X__00032

Identity

Accession:
OP596615 ↗
Kingdom:
phage

Quality

87.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bradyrhizobium_phage_ppBjS10J-1

TaxID: 3003365

Cluster

Singleton — not in a non-trivial cluster

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 7-161_245-256
PDB
Domain cluster: rep: IMGVR_UViG_3300009285_013394-3300009285-Ga0103680_100632362__D1-74_170-264
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4xtvB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 14.0 2.76e-01 80.2% 56.2%
6xgqb01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.66 37.0 4.78e-01 73.7% 97.8%
3vpbE00 2.20.28.160 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.57 22.0 3.57e-01 77.2% 100.0%
5tr9A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.55 27.0 3.37e-01 81.4% 76.0%
1zx5A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 24.0 3.33e-01 71.9% 83.1%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4512383 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 29.0 3.56e-01 88.6% 89.0%
D2 high residues 167-240
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a1rA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.79 61.0 5.86e-01 85.1% 71.8%
1xqbA01 2.40.30.70 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › YaeB-like 0.70 61.0 5.39e-01 97.3% 80.7%
1vq8B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.70 63.0 5.12e-01 100.0% 82.5%
6f2mA02 2.40.30.290 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.70 63.0 5.95e-01 100.0% 88.5%
4ac9C04 2.40.10.190 Mainly Beta › Beta Barrel › Thrombin, subunit H › translation elongation factor selb, chain A, domain 4 0.69 58.0 5.70e-01 100.0% 86.3%
2zzeA03 2.40.30.130 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.67 58.0 5.30e-01 100.0% 72.4%
2ey4D00 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.66 58.0 5.87e-01 100.0% 97.3%
2ra1A04 2.60.40.1220 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 56.0 5.14e-01 98.6% 75.3%
1fx0B01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.63 54.0 5.38e-01 100.0% 94.9%
3szeA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.63 55.0 3.65e-01 98.6% 37.3%
2vbkA00 2.160.20.10 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › Single-stranded right-handed beta-helix, Pectin lyase-like 0.62 49.0 3.01e-01 100.0% 12.9%
1vw3C01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 53.0 4.48e-01 100.0% 64.1%
3vmnA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 50.0 4.20e-01 100.0% 71.8%
3igfA02 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 44.0 4.48e-01 81.1% 95.9%
3kewA01 2.40.30.130 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 50.0 4.90e-01 100.0% 86.9%
2e7vA01 3.30.70.960 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › SEA domain 0.59 46.0 4.16e-01 87.8% 95.2%
4gaaA01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.59 47.0 3.53e-01 100.0% 34.2%
1j6wA00 3.30.1360.80 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › S-ribosylhomocysteinase (LuxS) 0.58 48.0 3.89e-01 97.3% 56.5%
2r6vA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 47.0 3.75e-01 93.2% 80.5%
3wdhA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 48.0 4.49e-01 97.3% 74.0%
2e8yA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 47.0 4.35e-01 98.6% 70.3%
1f0lA03 2.60.40.700 Mainly Beta › Sandwich › Immunoglobulin-like › Diphtheria toxin, receptor-binding domain 0.57 49.0 3.97e-01 100.0% 48.7%
4aeeA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 46.0 4.27e-01 98.6% 70.1%
4psrA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.57 47.0 4.16e-01 100.0% 61.5%
4ci2B02 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.56 40.0 3.44e-01 75.7% 92.0%
3w3sA01 3.30.70.1920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 44.0 3.43e-01 87.8% 47.6%
7zhdA01 3.20.80.10 Alpha Beta › Alpha-Beta Barrel › Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A › Regulatory factor, effector binding domain 0.55 43.0 3.55e-01 87.8% 83.8%
2pn5A10 2.60.40.690 Mainly Beta › Sandwich › Immunoglobulin-like › Alpha-macroglobulin, receptor-binding domain 0.54 45.0 3.68e-01 94.6% 70.5%
4dzdA01 3.30.70.1200 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 1 0.54 39.0 4.04e-01 85.1% 84.3%
1h3gA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 45.0 4.25e-01 97.3% 77.8%
2b5iB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 4.02e-01 97.3% 72.3%
7zgmA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 43.0 3.09e-01 94.6% 67.2%
3f8uD03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 43.0 3.94e-01 97.3% 82.1%
6cl5A01 2.60.40.3940 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 43.0 4.00e-01 100.0% 78.4%
1bf2A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 39.0 3.44e-01 82.4% 89.5%
1o7dC02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 42.0 4.06e-01 100.0% 80.9%
8owfA01 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.65e-01 100.0% 62.2%
2xdhA00 2.60.40.680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.46e-01 100.0% 50.7%
3w1eA01 3.30.1660.40 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › FlgT, N-terminal domain 0.50 36.0 3.44e-01 77.0% 95.6%
3bwsA01 2.60.40.3070 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 35.0 3.40e-01 89.2% 65.5%
5ldyA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 42.0 3.84e-01 98.6% 73.6%
1cwvA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 42.0 3.84e-01 97.3% 89.2%
4c0tA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 40.0 3.83e-01 93.2% 82.6%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3944437 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.76 69.0 6.78e-01 100.0% 92.5%
3600462 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.72 62.0 6.07e-01 100.0% 88.7%
5010595 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.71 63.0 6.08e-01 100.0% 89.4%
4945251 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.69 61.0 5.51e-01 100.0% 72.0%
5051893 1.1.7.20 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.69 62.0 6.06e-01 100.0% 95.0%
4942485 1.1.7.20 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.69 61.0 6.03e-01 100.0% 98.8%
5036479 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.69 61.0 5.33e-01 100.0% 65.5%
4214180 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.68 60.0 5.55e-01 100.0% 84.2%
5036581 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.67 57.0 5.21e-01 100.0% 70.0%
4391995 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.67 59.0 5.71e-01 100.0% 94.1%
3542635 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.67 59.0 4.89e-01 100.0% 65.2%
4066771 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.67 59.0 5.45e-01 100.0% 85.3%
5006437 70.2.1.6 ↗ beta barrels › beta-clip › dUTPase-like › dUTPase-like › DUF22 0.66 58.0 4.99e-01 100.0% 71.4%
4163756 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.65 57.0 5.29e-01 100.0% 85.3%
4491659 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.64 56.0 4.91e-01 100.0% 70.4%
4513211 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.64 56.0 4.82e-01 100.0% 77.5%
4186924 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.64 56.0 4.95e-01 100.0% 78.2%
3289956 4081.1.1.5 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N 0.64 47.0 3.57e-01 100.0% 30.8%
4114061 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.64 56.0 5.04e-01 100.0% 81.9%
4322439 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.64 55.0 4.85e-01 100.0% 65.5%
4886128 613.1.1.1 ↗ alpha complex topology › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › tRNA-synt_2c 0.64 55.0 4.91e-01 100.0% 78.2%
3604149 70.2.1.6 ↗ beta barrels › beta-clip › dUTPase-like › dUTPase-like › DUF22 0.63 55.0 5.03e-01 100.0% 84.0%
5022644 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 54.0 5.06e-01 100.0% 81.1%
4185030 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.63 55.0 5.09e-01 100.0% 83.2%
4416787 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.62 54.0 5.11e-01 100.0% 88.9%
4984453 4081.1.1.5 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N 0.61 46.0 3.45e-01 100.0% 30.8%
3604177 3386.2.1.0 ↗ beta sandwiches › gp9 C-terminal domain-like › gp10 domain 2 and domain 3 › gp10 domain 2 and domain 3 0.59 49.0 5.06e-01 100.0% 98.6%
3404732 304.9.1.95 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF4780 0.59 46.0 4.51e-01 86.5% 88.7%
5063755 4081.1.1.0 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.58 40.0 3.12e-01 98.6% 30.9%
5043609 4081.1.1.0 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.57 46.0 3.49e-01 100.0% 34.9%
4653283 4081.1.1.5 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N 0.57 46.0 3.41e-01 100.0% 32.4%
4955177 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.56 47.0 4.30e-01 100.0% 69.5%
3495353 221.13.1.1 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain › DUF4140 0.55 43.0 3.64e-01 100.0% 47.9%
5037021 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.54 46.0 4.22e-01 98.6% 75.0%
3285854 4182.1.1.0 ↗ beta sandwiches › Agglutinin HPA-like › Agglutinin HPA-like › Agglutinin HPA-like 0.54 44.0 3.85e-01 100.0% 81.4%
4996591 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.53 41.0 3.27e-01 87.8% 46.3%
5036913 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.52 41.0 3.91e-01 100.0% 74.4%
3277157 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 4.21e-01 100.0% 94.7%
3622189 11.1.1.297 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Integrin_A_Ig_2 0.52 39.0 3.26e-01 100.0% 42.7%
3625508 11.1.5.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › DUF7808 0.51 43.0 3.71e-01 100.0% 93.8%
5037360 10.20.1.0 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in cysteine protease › Jelly-roll domain in cysteine protease 0.51 43.0 3.81e-01 98.6% 90.4%
5054542 4081.1.1.12 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › DUF2207 0.51 40.0 3.26e-01 100.0% 41.2%
3286203 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 41.0 3.83e-01 100.0% 73.3%
5053692 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.50 42.0 3.31e-01 100.0% 46.1%
141846 4081.1.1.5 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N 0.50 40.0 3.06e-01 100.0% 33.5%