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NC_020868.1__YP_007676498.1__VPMG_00008__00008

Bact-Vir

NC_020868.1__YP_007676498.1__VPMG_00008__00008

Identity

Accession:
NC_020868 ↗
Kingdom:
phage

Quality

91.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Stoningtonvirus› Vibrio_phage_VBP32

TaxID: 754072

Cluster

View cluster (21 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 4-79
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3m7kA00 3.30.40.220 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › 0.83 75.0 6.06e-01 100.0% 70.4%
2qgpA00 1.10.30.50 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › 0.82 60.0 5.80e-01 76.3% 79.5%
5hsxB00 3.60.130.10 Alpha Beta › 4-Layer Sandwich › Double-stranded beta-helix › Clavaminate synthase-like 0.56 43.0 2.99e-01 85.5% 83.2%
3dzzA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.52 45.0 3.21e-01 98.7% 75.0%
3mc2A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 45.0 3.53e-01 100.0% 81.0%
3uw2A01 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.52 47.0 3.69e-01 100.0% 53.5%
2fd4A00 3.30.40.110 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › AvrPtoB, C-terminal domain 0.51 38.0 3.51e-01 88.2% 60.0%
2k2aA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.50 34.0 3.59e-01 100.0% 78.6%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
119462 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.82 75.0 6.04e-01 100.0% 70.4%
4979945 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.81 74.0 6.22e-01 100.0% 76.0%
185780 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.81 60.0 5.55e-01 78.9% 70.1%
3397473 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.78 67.0 5.76e-01 94.7% 65.0%
3879791 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.76 68.0 4.86e-01 100.0% 36.4%
3561303 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.76 68.0 5.26e-01 100.0% 49.7%
5070853 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.76 57.0 5.47e-01 78.9% 72.9%
3489023 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.74 66.0 5.68e-01 100.0% 69.2%
4959591 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.74 52.0 5.59e-01 89.5% 86.2%
3952776 377.1.1.88 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › HNH 0.71 52.0 5.53e-01 80.3% 89.2%
3587782 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.71 60.0 5.28e-01 100.0% 63.6%
3953059 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.70 51.0 4.83e-01 80.3% 64.4%
4492949 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.70 52.0 4.68e-01 84.2% 57.1%
4938470 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.69 44.0 4.12e-01 90.8% 54.4%
4994221 4020.1.1.3 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › TFX_C 0.69 53.0 5.56e-01 90.8% 90.0%
3211768 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.68 41.0 3.68e-01 81.6% 43.8%
3249964 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.67 52.0 5.16e-01 89.5% 78.8%
4154381 148.1.3.8 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › ClpB_D2-small 0.64 51.0 4.88e-01 88.2% 95.6%
4509297 532.2.1.0 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.57 52.0 3.74e-01 98.7% 72.2%
3614843 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.55 41.0 2.37e-01 80.3% 11.2%
3235148 221.1.1.58 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › CRIM 0.52 39.0 3.47e-01 81.6% 60.9%
3176813 148.1.1.74 ↗ alpha arrays › Histone-like › Histone-related › Histone › PF29498 0.50 45.0 3.90e-01 98.7% 76.3%
3176836 193.1.1.50 ↗ alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › PF29498 0.50 37.0 3.25e-01 94.7% 52.7%
D2 medium residues 89-117
PDB
Domain cluster: representative