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NC_019713.1__YP_007111849.1__F862_gp011__00003

Bact-Vir

NC_019713.1__YP_007111849.1__F862_gp011__00003

Identity

Accession:
NC_019713 ↗
Kingdom:
phage

Quality

75.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Mardecavirus› Vibrio_phage_vB_VpaS_MAR10

TaxID: 1229755

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 4-109
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2bzyA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.60 23.0 2.91e-01 77.4% 53.2%
3c0wA02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.58 34.0 3.48e-01 77.4% 58.3%
2ej9A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 40.0 3.34e-01 74.5% 62.2%
2h2yA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.55 36.0 3.55e-01 94.3% 61.2%
5w2fA01 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.54 32.0 3.53e-01 73.6% 72.1%
2q7eA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 43.0 3.55e-01 89.6% 85.8%
1j5wB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 42.0 3.56e-01 88.7% 80.1%
1tkjA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 46.0 3.49e-01 100.0% 78.3%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.52 41.0 4.17e-01 95.3% 87.0%
2cy9B00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 44.0 4.17e-01 95.3% 88.6%
1k3eB02 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 36.0 3.65e-01 91.5% 72.4%
2dt9A01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.51 32.0 3.69e-01 74.5% 89.2%
5k8pD01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.51 44.0 3.30e-01 100.0% 85.0%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4323652 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 38.0 3.82e-01 76.4% 59.0%
3881061 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 38.0 4.67e-01 77.4% 96.9%
3894482 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.61 49.0 3.70e-01 88.7% 77.1%
5080958 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 0.60 38.0 4.23e-01 98.1% 88.0%
3950413 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.58 37.0 3.67e-01 78.3% 61.8%
3402001 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.56 39.0 4.19e-01 70.8% 94.4%
3921260 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 39.0 3.72e-01 85.8% 64.2%
1125246 306.3.1.2 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › Img2 0.55 32.0 3.69e-01 73.6% 78.9%
4017316 304.8.1.10 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_7 0.54 30.0 2.60e-01 75.5% 31.4%
4086765 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.54 35.0 3.52e-01 77.4% 63.6%
4096306 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.53 36.0 3.58e-01 80.2% 65.2%
4389430 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.53 36.0 3.58e-01 79.2% 67.3%
4934117 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.52 34.0 3.75e-01 77.4% 83.5%
4221596 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.52 35.0 3.42e-01 78.3% 62.6%
4683313 242.1.1.5 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.51 35.0 3.40e-01 79.2% 61.7%
3701084 316.1.1.14 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › LicD 0.51 45.0 3.78e-01 100.0% 75.7%
4944556 225.1.1.0 ↗ 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 0.51 36.0 3.29e-01 72.6% 57.1%
3596133 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 0.51 40.0 4.14e-01 87.7% 90.0%
4963468 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.51 37.0 3.81e-01 84.0% 80.0%
3280463 3513.1.1.0 ↗ a+b two layers › Putative lipoprotein LppA › Putative lipoprotein LppA › Putative lipoprotein LppA 0.50 40.0 3.73e-01 86.8% 86.7%
3629581 7512.1.1.6 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_20 0.50 38.0 2.83e-01 80.2% 59.3%
3957864 881.1.1.17 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › DUF3710 0.50 38.0 3.29e-01 80.2% 74.7%