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NC_031004.1__YP_009277935.1__BIZ68_gp17__00017

Bact-Vir

NC_031004.1__YP_009277935.1__BIZ68_gp17__00017

Identity

Accession:
NC_031004 ↗
Kingdom:
phage

Quality

89.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nyceiraevirus› Gordonia_phage_Nyceirae

TaxID: 1887651

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 5-154
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.82 66.0 7.11e-01 100.0% 96.9%
3fz2A00 3.30.70.1700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phage minor tail protein U 0.75 59.0 6.33e-01 100.0% 95.3%
4acvA00 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.75 56.0 6.20e-01 100.0% 97.5%
4frwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.71 33.0 4.04e-01 75.3% 67.7%
2w59B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 36.0 4.11e-01 76.7% 70.2%
1cqkA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 33.0 3.96e-01 76.7% 73.3%
1kcvL02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 34.0 3.99e-01 76.7% 76.7%
4o5lL02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 33.0 3.82e-01 76.7% 73.1%
1ohgA01 3.30.2400.10 Alpha Beta › 2-Layer Sandwich › Major capsid protein gp5 fold › Major capsid protein gp5 0.59 41.0 4.17e-01 70.7% 92.5%
2nyiA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 31.0 3.85e-01 86.7% 83.3%
2c1iA01 3.30.565.50 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › 0.57 30.0 3.46e-01 100.0% 68.5%
6i9gA01 3.30.2400.30 Alpha Beta › 2-Layer Sandwich › Major capsid protein gp5 fold › 0.57 39.0 3.81e-01 70.7% 73.4%
3pfeA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 37.0 3.98e-01 93.3% 77.7%
3qw9B00 2.60.40.4100 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-C domain 0.54 38.0 3.68e-01 76.7% 63.9%
3qkbA00 3.30.110.70 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Hypothetical protein apc22750. Chain B 0.54 34.0 4.13e-01 95.3% 98.9%
2ebeA00 3.30.70.2290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Protein of unknown function (DUF3208) 0.54 33.0 3.83e-01 96.0% 86.8%
2wyhA05 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 34.0 3.60e-01 96.0% 73.1%
3rqwA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.51 46.0 4.28e-01 100.0% 93.7%
2bg9C01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.51 36.0 3.29e-01 92.0% 52.6%
6y1zA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.51 46.0 4.12e-01 100.0% 79.7%
6d6tA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.51 36.0 3.26e-01 91.3% 52.4%
3u83A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 33.0 4.02e-01 77.3% 100.0%
6ofsA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.50 42.0 3.97e-01 90.0% 83.2%
1w7cA03 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 31.0 3.51e-01 82.7% 80.0%
ECOD (31)
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 0.88 70.0 7.65e-01 100.0% 97.6%
5083619 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.75 64.0 6.60e-01 100.0% 94.4%
364035 304.124.1.1 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_U 0.73 58.0 6.15e-01 99.3% 93.2%
5040945 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.73 63.0 6.32e-01 100.0% 91.3%
3589403 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.72 55.0 6.06e-01 98.0% 97.5%
3825541 304.8.1.45 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.66 36.0 4.07e-01 78.7% 69.1%
2785992 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.65 34.0 4.06e-01 76.7% 73.1%
4827386 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.65 35.0 3.79e-01 76.7% 61.3%
4970968 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.64 42.0 4.78e-01 72.0% 88.5%
3025552 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.64 35.0 3.97e-01 76.7% 70.3%
169956 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.63 36.0 4.13e-01 76.7% 75.0%
4440592 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 0.56 50.0 4.38e-01 97.3% 89.3%
3463183 304.25.1.0 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain 0.56 38.0 4.14e-01 91.3% 85.0%
5081487 2485.3.1.10 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF5309 0.56 39.0 3.17e-01 70.7% 91.6%
4988094 2485.3.1.18 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 0.54 38.0 3.20e-01 70.7% 82.7%
3993884 331.9.1.0 ↗ a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.54 38.0 3.77e-01 72.0% 81.1%
4241362 2485.3.1.0 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 0.54 37.0 2.99e-01 70.0% 84.4%
3701983 304.153.1.0 ↗ a+b two layers › Alpha-beta plaits › Collagenase G catalytic helper subdomain › Collagenase G catalytic helper subdomain 0.54 49.0 4.64e-01 99.3% 94.3%
3705145 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 0.53 48.0 4.54e-01 100.0% 93.9%
3537321 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.53 34.0 4.08e-01 76.7% 97.0%
3229892 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 47.0 4.13e-01 100.0% 82.6%
3474068 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 47.0 4.06e-01 100.0% 81.7%
4522769 212.1.1.9 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › DNA_mis_repair 0.52 33.0 3.39e-01 90.0% 66.2%
3481119 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.52 47.0 4.16e-01 100.0% 78.6%
3495127 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 0.51 47.0 3.85e-01 100.0% 70.5%
4451360 12.3.1.24 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › YidC_periplas 0.51 46.0 3.86e-01 100.0% 88.5%
2995325 2485.3.1.9 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF4043 0.51 43.0 3.23e-01 91.3% 87.0%
3992699 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 0.51 46.0 4.00e-01 100.0% 83.0%
3493567 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 0.50 46.0 3.95e-01 100.0% 83.0%
3934879 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 0.50 46.0 3.93e-01 100.0% 70.4%
4157506 11.1.1.100 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set,C2-set_2 0.50 30.0 2.57e-01 75.3% 36.6%