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NC_015721.1__YP_004678852.1__BdPhPhi1402_gp25__00025

Bact-Vir

NC_015721.1__YP_004678852.1__BdPhPhi1402_gp25__00025

Identity

Accession:
NC_015721 ↗
Kingdom:
phage

Quality

76.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bdellovibrio_phage_phi1402

TaxID: 1035662

Cluster

View cluster (24 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 52-170
PDB
Domain cluster: rep: OP947159.1__WBC28288.1__DPMD02_24__00025__D7-135
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wruA01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.80 52.0 4.54e-01 99.2% 45.1%
1dr9A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 40.0 4.42e-01 93.3% 70.5%
1t7vA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 39.0 4.41e-01 90.8% 73.3%
4wsqB00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.68 43.0 3.12e-01 95.8% 24.2%
3o1lB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.67 37.0 4.23e-01 85.7% 72.7%
3d37B01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.66 46.0 4.05e-01 100.0% 48.9%
1y12B00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.66 59.0 5.36e-01 99.2% 73.7%
2x8kA01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.66 48.0 5.04e-01 99.2% 85.7%
4divV01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.65 58.0 5.59e-01 99.2% 85.4%
3kyfA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.65 41.0 4.20e-01 100.0% 65.0%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.65 36.0 4.16e-01 85.7% 75.0%
1ygyA04 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 34.0 4.13e-01 86.6% 78.9%
4w64B00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.64 58.0 5.28e-01 100.0% 75.0%
4q7aC02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 40.0 4.19e-01 90.8% 69.4%
2w59A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 37.0 4.04e-01 93.3% 70.0%
5xyiU00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 41.0 4.48e-01 87.4% 82.5%
4hkhA00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.62 57.0 5.26e-01 100.0% 79.9%
6ue9L02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 38.0 3.80e-01 90.8% 61.5%
2rb7A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 37.0 3.88e-01 86.6% 67.3%
1ya5T01 2.20.160.10 Mainly Beta › Single Sheet › titin filament fold › titin domain like 0.59 32.0 3.78e-01 86.6% 75.0%
3g88A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 37.0 2.92e-01 95.0% 31.0%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.57 50.0 4.81e-01 99.2% 83.8%
3ct9A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 35.0 3.70e-01 84.9% 68.2%
1qzzA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 35.0 3.14e-01 95.8% 43.8%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.56 48.0 4.70e-01 99.2% 86.2%
6ofsA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.54 36.0 3.17e-01 85.7% 44.0%
1vm0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.54 34.0 3.83e-01 95.0% 81.7%
1y0hB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 34.0 3.68e-01 89.9% 75.5%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 35.0 3.62e-01 84.9% 70.2%
1nvmB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 48.0 4.35e-01 97.5% 90.3%
7rsfA01 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 37.0 3.71e-01 84.0% 71.9%
3qw9B00 2.60.40.4100 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-C domain 0.52 42.0 3.75e-01 92.4% 62.0%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3969448 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.79 65.0 6.95e-01 97.5% 99.0%
3604610 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.78 43.0 5.64e-01 85.7% 98.5%
3580020 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.77 72.0 6.00e-01 100.0% 72.8%
3943681 1.1.13.47 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Dit_like 0.77 72.0 6.59e-01 100.0% 84.7%
4988102 1.1.13.47 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Dit_like 0.75 62.0 6.41e-01 98.3% 92.7%
3980535 1.1.13.51 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_P2_GpU 0.73 66.0 6.31e-01 99.2% 85.9%
4157825 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.72 65.0 6.34e-01 99.2% 88.5%
2642579 1.1.13.6 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tail_2 0.72 62.0 6.08e-01 99.2% 85.4%
2468519 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.71 54.0 5.83e-01 99.2% 92.2%
3965192 1.1.13.67 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF2460 0.71 62.0 6.40e-01 97.5% 97.4%
5004308 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.71 66.0 5.99e-01 100.0% 78.7%
3164699 1.1.13.33 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DNA_circ_N 0.70 59.0 6.08e-01 98.3% 93.9%
3190573 706.2.1.0 ↗ beta complex topology › Head domain of nucleotide exchange factor GrpE › G5 and E repeats in surface protein G › G5 and E repeats in surface protein G 0.70 34.0 4.74e-01 95.0% 100.0%
4873215 1.1.13.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF2001 0.68 61.0 5.74e-01 98.3% 81.4%
3905413 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.68 40.0 4.25e-01 90.8% 65.7%
3964955 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.68 63.0 5.63e-01 100.0% 80.0%
184986 1.1.13.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Sipho_tail 0.63 55.0 5.47e-01 99.2% 91.9%
5071836 512.1.1.1 ↗ 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_1st 0.61 30.0 3.49e-01 95.8% 63.3%
3928940 241.6.1.1 ↗ a+b two layers › Type III secretory system chaperone-like › Arp2/3 complex subunits › Arp2/3 complex subunits › P34-Arc 0.61 42.0 3.75e-01 94.1% 50.9%
3959045 305.1.1.0 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.59 46.0 4.61e-01 93.3% 80.0%
3289660 305.1.1.3 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › DUF3000 0.59 46.0 4.59e-01 93.3% 80.0%
3934459 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 35.0 3.80e-01 90.8% 70.0%
3353115 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.58 42.0 3.23e-01 95.0% 34.2%
4136515 310.3.1.23 ↗ 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 › RP854 0.57 48.0 4.39e-01 97.5% 68.8%
5004177 304.124.1.3 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.57 50.0 4.98e-01 98.3% 92.0%
4163084 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.57 37.0 3.80e-01 90.8% 68.7%
4261744 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.56 51.0 5.06e-01 99.2% 94.4%
4943141 304.25.1.0 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain 0.56 39.0 3.90e-01 91.6% 69.2%
3585212 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.56 51.0 4.17e-01 99.2% 82.8%
2126271 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.56 36.0 3.72e-01 89.9% 67.0%
5010248 512.1.1.1 ↗ 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_1st 0.56 30.0 3.53e-01 96.6% 75.0%
2642577 304.124.1.3 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.56 48.0 4.64e-01 99.2% 83.6%
4954550 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 0.55 42.0 4.34e-01 98.3% 84.3%
4935602 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 35.0 3.56e-01 90.8% 65.8%
4961272 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 37.0 3.78e-01 91.6% 72.5%
4987575 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 34.0 3.59e-01 92.4% 70.0%
3593428 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.53 45.0 3.14e-01 95.8% 28.2%
4971865 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 36.0 3.67e-01 91.6% 70.0%
4999156 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 36.0 3.66e-01 85.7% 71.3%
4055405 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.52 38.0 3.76e-01 89.9% 72.8%
4481559 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.52 38.0 3.73e-01 90.8% 70.8%
5048630 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.51 38.0 3.66e-01 86.6% 68.1%
3210401 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.51 38.0 2.61e-01 88.2% 22.1%
4969658 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.51 34.0 3.52e-01 91.6% 70.4%
4021762 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.51 39.0 2.45e-01 79.8% 34.3%
3717787 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.50 37.0 2.58e-01 76.5% 71.1%