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OP947161.1__WBC28471.1__RPMD05_84__00085

Bact-Vir

OP947161.1__WBC28471.1__RPMD05_84__00085

Identity

Accession:
OP947161 ↗
Kingdom:
phage

Quality

77.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodobacteraceae_phage_LS06-2018-MD05

TaxID: 3003838

Cluster

View cluster (4 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 3-128
PDB
Domain cluster: rep: OQ326496.2__WDQ45522.1__X__00066__D7-128
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vqeE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.69 27.0 3.79e-01 78.6% 71.9%
1vf7F01 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.63 43.0 4.66e-01 81.7% 85.3%
4w64B00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.63 56.0 5.23e-01 100.0% 97.5%
1dr9A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 35.0 3.91e-01 78.6% 72.6%
5yppA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 31.0 3.60e-01 77.0% 67.8%
4divV01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 49.0 4.81e-01 91.3% 92.0%
5oj2B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 33.0 3.72e-01 76.2% 71.9%
3q0bX00 2.30.280.10 Mainly Beta › Roll › PUA domain-like › SRA-YDG 0.57 48.0 4.58e-01 91.3% 85.1%
1dq3A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.56 34.0 3.89e-01 81.0% 85.1%
4z1xA02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 35.0 3.36e-01 81.7% 55.2%
2joqA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 28.0 3.42e-01 75.4% 78.7%
2pb7A01 2.30.280.10 Mainly Beta › Roll › PUA domain-like › SRA-YDG 0.54 44.0 4.01e-01 90.5% 74.0%
3ue2A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 29.0 3.36e-01 75.4% 72.7%
3f02B02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.53 29.0 3.24e-01 92.1% 66.0%
6lynD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 29.0 3.35e-01 80.2% 73.6%
4dpoB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 30.0 3.32e-01 71.4% 68.3%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.52 43.0 4.29e-01 89.7% 98.5%
4jb9H01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.65e-01 80.2% 71.0%
4bhqA00 3.30.70.2830 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 4.02e-01 91.3% 90.8%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2674670 1.1.13.6 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tail_2 0.72 61.0 5.47e-01 90.5% 73.8%
4140243 1.1.5.82 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF2001 0.69 54.0 5.68e-01 90.5% 90.4%
5002750 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.68 52.0 5.68e-01 87.3% 97.1%
4957560 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.66 55.0 5.52e-01 89.7% 94.6%
3936663 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.65 49.0 4.92e-01 86.5% 78.4%
3387224 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.64 40.0 4.03e-01 92.1% 61.5%
3058416 1.1.5.39 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › TssD 0.64 57.0 5.74e-01 98.4% 97.6%
3942090 1.1.5.77 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Phage_tube 0.63 57.0 5.23e-01 100.0% 98.2%
2642579 1.1.13.6 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tail_2 0.63 53.0 5.27e-01 91.3% 92.3%
4957565 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.63 52.0 5.23e-01 87.3% 96.0%
5011662 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 49.0 4.62e-01 82.5% 76.0%
3944430 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.60 46.0 5.04e-01 91.3% 97.1%
3659065 304.8.1.45 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.60 36.0 3.95e-01 78.6% 72.0%
3224729 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 43.0 4.82e-01 86.5% 100.0%
4609849 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.58 36.0 4.12e-01 87.3% 84.4%
4083039 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 38.0 4.00e-01 80.2% 73.0%
3933059 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.57 35.0 3.71e-01 90.5% 67.0%
3369744 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.57 34.0 3.59e-01 81.0% 63.5%
3206671 242.1.1.1 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.57 35.0 3.49e-01 81.7% 58.5%
3868052 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.57 47.0 4.52e-01 89.7% 97.2%
3529818 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.56 47.0 4.44e-01 90.5% 95.3%
5556 242.1.1.4 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › Endonuc_subdom 0.56 34.0 3.78e-01 81.7% 77.6%
4942056 11.4.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Antigen MPT63/MPB63 (immunoprotective extracellular protein) › Antigen MPT63/MPB63 (immunoprotective extracellular protein) 0.55 38.0 3.67e-01 90.5% 62.9%
3409790 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.54 32.0 2.52e-01 76.2% 26.5%
3604601 11.4.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Antigen MPT63/MPB63 (immunoprotective extracellular protein) › Antigen MPT63/MPB63 (immunoprotective extracellular protein) 0.54 37.0 3.83e-01 90.5% 74.2%
3333639 11.1.1.51 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › LEA_2 0.53 37.0 3.57e-01 82.5% 61.4%
3942981 2484.1.1.269 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_4 0.52 38.0 2.76e-01 75.4% 50.3%
4937023 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.52 31.0 3.44e-01 90.5% 73.0%
D2 high residues 157-189_204-342
PDB
D3 high residues 451-464_641-723
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1k28D03 2.40.30.150 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacteriophage T4, Gp27, baseplate hub, domain 3 0.62 49.0 4.97e-01 83.5% 94.7%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.62 49.0 4.58e-01 84.5% 69.7%
2vgmA01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.61 40.0 3.69e-01 86.6% 52.5%
3obyA01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.61 37.0 3.56e-01 83.5% 53.2%
2ecuA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 47.0 4.10e-01 83.5% 72.5%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 47.0 4.41e-01 84.5% 78.2%
2p5zX01 2.30.110.50 Mainly Beta › Roll › Pnp Oxidase; Chain A › 0.60 45.0 3.74e-01 78.4% 49.4%
5choF00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 46.0 3.94e-01 83.5% 75.0%
3pftA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 46.0 3.95e-01 83.5% 74.4%
3nfwA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 46.0 3.77e-01 83.5% 64.8%
3e4vA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 46.0 3.78e-01 84.5% 71.3%
1vf7F01 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.57 44.0 4.33e-01 81.4% 85.3%
3fppA01 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.56 40.0 3.98e-01 81.4% 70.2%
5escA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 44.0 4.15e-01 85.6% 86.6%
1r5bA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.54 38.0 3.97e-01 80.4% 79.8%
3wbiA04 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 41.0 3.65e-01 84.5% 59.3%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 47.0 4.47e-01 100.0% 97.4%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 39.0 3.89e-01 82.5% 79.0%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 36.0 3.22e-01 73.2% 67.4%
3h7tA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 38.0 3.66e-01 81.4% 68.5%
2qy0B02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.50 38.0 3.75e-01 81.4% 75.0%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3981654 1.1.13.40 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_min_tail 0.71 56.0 5.36e-01 83.5% 97.3%
3603127 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.67 50.0 5.24e-01 79.4% 93.3%
3219406 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.66 35.0 4.60e-01 80.4% 98.0%
4399696 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.62 48.0 4.86e-01 81.4% 97.9%
5001719 1.1.9.50 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › PF28530 0.62 50.0 4.75e-01 87.6% 95.7%
4414535 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.62 48.0 4.80e-01 83.5% 94.0%
4323001 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.61 48.0 4.78e-01 83.5% 96.0%
4197939 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.61 46.0 4.72e-01 80.4% 95.8%
4618294 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.61 46.0 4.72e-01 81.4% 96.8%
3590379 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.61 45.0 4.72e-01 79.4% 90.0%
4597893 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 47.0 4.70e-01 83.5% 96.0%
4168875 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 47.0 4.77e-01 83.5% 94.7%
4246654 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 47.0 4.72e-01 84.5% 96.0%
5012011 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 48.0 4.48e-01 87.6% 85.6%
3278636 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.60 47.0 4.01e-01 83.5% 76.1%
4452640 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 46.0 4.68e-01 82.5% 95.8%
4031753 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.60 44.0 4.44e-01 81.4% 78.9%
3950388 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.59 46.0 4.06e-01 84.5% 80.4%
3286692 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.59 47.0 4.67e-01 84.5% 94.0%
4197235 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.59 45.0 4.60e-01 81.4% 96.8%
4139867 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.59 45.0 4.58e-01 81.4% 96.8%
3626966 1.1.7.90 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ZNFX1 0.59 45.0 4.31e-01 81.4% 72.7%
4565791 1.1.7.87 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25954 0.58 42.0 4.33e-01 82.5% 81.1%
3264338 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 39.0 4.03e-01 80.4% 73.3%
4452931 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.58 44.0 4.35e-01 83.5% 93.3%
3387966 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 39.0 4.17e-01 81.4% 82.4%
4234915 1.1.5.26 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZN 0.57 44.0 4.23e-01 84.5% 72.2%
3265100 1.1.7.90 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ZNFX1 0.56 43.0 4.08e-01 84.5% 69.6%
4946798 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 41.0 4.14e-01 81.4% 77.0%
3884573 11.1.1.318 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL3Rb_N 0.55 37.0 3.87e-01 78.4% 74.4%
3170371 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.55 42.0 3.94e-01 82.5% 80.0%
3535347 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.54 41.0 3.95e-01 82.5% 82.6%
3262455 1.1.7.90 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ZNFX1 0.54 41.0 4.11e-01 83.5% 79.0%
3511826 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.54 41.0 4.01e-01 82.5% 74.3%
5018908 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.53 47.0 4.28e-01 100.0% 82.2%
3500556 3775.1.1.1 ↗ beta barrels › Lysosome membrane protein 2 lumenal domain › Lysosome membrane protein 2 lumenal domain › Lysosome membrane protein 2 lumenal domain › CD36 0.52 32.0 2.12e-01 84.5% 14.0%
3504294 1.1.7.27 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › DUF1905 0.51 36.0 3.74e-01 81.4% 80.0%
3594165 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 40.0 3.34e-01 84.5% 55.3%
3261993 11.1.1.843 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7034 0.51 39.0 3.69e-01 81.4% 70.4%
D4 medium residues 129-156_368-436
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5y0uA02 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.52 21.0 3.28e-01 90.7% 100.0%
D5 medium residues 468-640
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ak1A01 2.60.40.2710 Mainly Beta › Sandwich › Immunoglobulin-like › BT4661 domain 1 0.53 24.0 3.09e-01 87.3% 73.7%