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NC_031108.1__YP_009290916.1__BI041_gp09__00009

Bact-Vir

NC_031108.1__YP_009290916.1__BI041_gp09__00009

Identity

Accession:
NC_031108 ↗
Kingdom:
phage

Quality

93.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pulverervirus› Propionibacterium_phage_PFR2

TaxID: 1838138

Cluster

View cluster (351 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 11-135
PDB
Domain cluster: rep: NC_024392.1__YP_009045168.1__LP114_114__00113__D16-138
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4acvA00 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.84 70.0 7.18e-01 100.0% 91.6%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.78 73.0 7.23e-01 100.0% 96.9%
3fz2A00 3.30.70.1700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phage minor tail protein U 0.74 67.0 6.67e-01 100.0% 95.3%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.73 69.0 6.67e-01 100.0% 91.2%
2xzmP00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 42.0 3.94e-01 88.0% 49.3%
5xyiY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 39.0 4.30e-01 76.0% 66.7%
2rjzA02 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.69 49.0 5.38e-01 100.0% 91.9%
5optY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 42.0 4.27e-01 80.0% 64.2%
4q97A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 40.0 4.31e-01 80.0% 71.3%
3of6E00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 40.0 4.41e-01 80.0% 75.0%
6ue9L02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 41.0 4.17e-01 80.0% 66.4%
5e4bA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.62 47.0 4.19e-01 80.0% 87.5%
3vzhA00 3.30.70.2660 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 46.0 3.93e-01 79.2% 53.1%
6nhiA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 54.0 3.91e-01 100.0% 96.5%
1z7mC00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 54.0 4.04e-01 100.0% 92.4%
2cjaA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 53.0 3.95e-01 100.0% 80.9%
3netB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 53.0 3.95e-01 100.0% 94.0%
4g84A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.58 53.0 3.87e-01 100.0% 91.6%
3pg1A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 39.0 3.96e-01 85.6% 66.7%
1httA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.58 53.0 4.10e-01 100.0% 92.9%
3racA00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 51.0 3.76e-01 100.0% 92.0%
6iy8A01 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.57 42.0 3.69e-01 98.4% 51.3%
2q7eA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 50.0 4.25e-01 100.0% 95.8%
3nrfA00 2.60.40.4110 Mainly Beta › Sandwich › Immunoglobulin-like › Protein of unknown function DUF4354 0.56 38.0 4.12e-01 80.0% 84.3%
1usyC00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 50.0 3.88e-01 98.4% 98.9%
3otlA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 40.0 3.76e-01 74.4% 86.9%
1b7yA00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 50.0 3.94e-01 100.0% 91.7%
6dw1A00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.55 49.0 4.19e-01 100.0% 81.0%
3u6yA00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.55 40.0 4.40e-01 98.4% 93.9%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.55 50.0 3.86e-01 100.0% 94.9%
2e3nA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 44.0 3.60e-01 86.4% 71.9%
3rqwA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 48.0 4.20e-01 100.0% 92.1%
2bg9C01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 49.0 4.12e-01 100.0% 78.0%
3jafA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 48.0 4.07e-01 100.0% 81.5%
6d6tA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 48.0 4.08e-01 100.0% 80.0%
5afoA01 2.60.40.1090 Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrial-type adhesion domain 0.54 40.0 3.75e-01 79.2% 98.8%
1iamA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 34.0 4.16e-01 79.2% 98.8%
2xzmJ00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.52 37.0 3.94e-01 84.0% 86.7%
2wyhA05 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 38.0 3.81e-01 96.0% 73.9%
3qfgA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 42.0 4.03e-01 90.4% 75.9%
1omsA00 3.30.70.1050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain 0.51 38.0 3.94e-01 77.6% 100.0%
4frwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 4.12e-01 78.4% 97.9%
5ixgA00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.51 38.0 3.49e-01 79.2% 82.7%
3nqkA02 2.40.128.440 Mainly Beta › Beta Barrel › Lipocalin › Uncharacterised protein PF14274, DUF4361 0.51 38.0 3.54e-01 79.2% 74.4%
3igqC00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.50 44.0 3.96e-01 100.0% 86.4%
2oznA00 2.60.40.680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 37.0 3.62e-01 80.0% 71.4%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004177 304.124.1.3 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.87 82.0 8.24e-01 100.0% 97.6%
3941902 304.124.1.7 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Minor_capsid_3 0.84 78.0 7.89e-01 100.0% 98.4%
4883824 304.124.1.6 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF5072 0.80 69.0 6.84e-01 100.0% 88.4%
2642577 304.124.1.3 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.78 73.0 7.15e-01 100.0% 94.0%
5083619 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.77 71.0 6.83e-01 100.0% 94.4%
3972055 11.1.1.410 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › BatD 0.76 47.0 4.78e-01 77.6% 63.3%
5083880 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.74 68.0 6.47e-01 100.0% 97.2%
4291659 304.124.1.8 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_Mu_Gp37 0.73 69.0 6.60e-01 100.0% 95.0%
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 0.73 57.0 5.98e-01 100.0% 91.3%
364035 304.124.1.1 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_U 0.71 66.0 6.46e-01 100.0% 94.0%
4206503 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.71 43.0 4.38e-01 79.2% 62.5%
4296415 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.71 43.0 4.73e-01 90.4% 75.0%
4854085 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.70 42.0 4.43e-01 77.6% 65.5%
4066506 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.70 42.0 4.54e-01 88.8% 70.5%
3472001 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.68 40.0 4.25e-01 89.6% 64.3%
3267312 11.1.5.62 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › CBM49 0.66 44.0 5.00e-01 79.2% 89.5%
3353115 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.64 46.0 3.60e-01 100.0% 35.8%
3505875 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.63 42.0 3.18e-01 85.6% 28.5%
3478508 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.62 43.0 3.93e-01 72.0% 84.1%
4562028 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 0.62 49.0 4.72e-01 100.0% 73.8%
3232555 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.60 45.0 3.93e-01 80.0% 52.1%
3559721 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.60 43.0 3.76e-01 73.6% 87.6%
None — 0.60 54.0 3.98e-01 100.0% 91.8%
1346899 304.158.1.2 ↗ a+b two layers › Alpha-beta plaits › CRISPR system Cas5 homologs › CRISPR system Cas5 homologs › Cas_Cas5d 0.59 45.0 3.74e-01 79.2% 49.1%
5030573 314.1.1.9 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.59 54.0 3.95e-01 100.0% 92.5%
4500953 314.1.1.9 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.59 54.0 4.04e-01 100.0% 92.3%
3786844 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 3.94e-01 80.0% 67.2%
4995818 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.58 48.0 4.83e-01 99.2% 88.8%
3581757 11.12.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD,Neur_chan_memb 0.58 44.0 3.65e-01 80.0% 54.7%
3510509 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.58 44.0 4.11e-01 80.0% 65.2%
None — 0.58 53.0 4.11e-01 100.0% 77.4%
4588058 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.58 53.0 4.08e-01 100.0% 75.2%
4931376 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.58 53.0 4.55e-01 100.0% 94.8%
3477231 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 52.0 4.37e-01 99.2% 66.8%
3613662 304.102.1.3 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_1 0.57 45.0 3.29e-01 85.6% 49.1%
None — 0.57 51.0 3.43e-01 100.0% 53.7%
3621533 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.56 50.0 4.20e-01 100.0% 80.0%
3181792 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.56 40.0 3.45e-01 72.8% 79.0%
4098100 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.56 50.0 3.96e-01 100.0% 94.3%
3517061 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.56 49.0 4.27e-01 99.2% 91.8%
4340137 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 44.0 3.29e-01 86.4% 45.5%
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 0.55 48.0 4.46e-01 97.6% 76.2%
3643481 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 44.0 3.13e-01 86.4% 42.1%
3924477 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.54 43.0 4.18e-01 87.2% 84.8%
4945893 328.1.1.0 ↗ a+b two layers › IF3-like › AlbA-like › AlbA-like 0.54 37.0 4.20e-01 99.2% 96.7%
3936287 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.54 49.0 4.13e-01 100.0% 82.3%
3634674 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.54 42.0 3.08e-01 84.0% 80.0%
3622783 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.53 48.0 3.97e-01 100.0% 84.9%
3258612 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.53 48.0 4.75e-01 96.8% 94.6%
3389007 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.53 47.0 4.10e-01 98.4% 81.0%
3923409 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.53 47.0 3.89e-01 100.0% 76.5%
5046532 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 3.99e-01 90.4% 74.8%
3800011 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.52 46.0 4.00e-01 100.0% 82.4%
3739749 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.52 47.0 4.24e-01 100.0% 92.9%
3806477 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.51 46.0 4.14e-01 96.8% 90.0%
3972919 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.51 38.0 3.88e-01 78.4% 92.0%
3311773 880.1.1.1 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.51 43.0 2.90e-01 90.4% 82.7%
3272662 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.50 45.0 3.42e-01 98.4% 98.0%