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NC_031017.1__YP_009279691.1__BI029_gp11__00011

Bact-Vir

NC_031017.1__YP_009279691.1__BI029_gp11__00011

Identity

Accession:
NC_031017 ↗
Kingdom:
phage

Quality

79.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lactococcus_phage_63301

TaxID: 1871687

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 9-93
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.68 46.0 5.10e-01 75.3% 88.1%
3lynB00 1.20.150.10 Mainly Alpha › Up-down Bundle › Lysin › Fertilization protein 0.65 49.0 4.34e-01 80.0% 78.2%
1ybzA00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.64 29.0 3.13e-01 81.2% 47.4%
8h4pA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.61 55.0 3.73e-01 100.0% 62.6%
2c9oB03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.60 49.0 5.00e-01 94.1% 92.8%
1guxB00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.59 53.0 4.50e-01 100.0% 82.3%
1jt6A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 41.0 3.57e-01 72.9% 74.5%
2gdzA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 52.0 3.69e-01 100.0% 90.2%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 40.0 4.06e-01 71.8% 72.6%
2fq4A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 42.0 3.64e-01 100.0% 48.2%
3uk6A02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.57 46.0 4.68e-01 95.3% 92.8%
3vw4A01 1.10.340.50 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › 0.57 36.0 3.53e-01 92.9% 58.7%
1ks9A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.56 38.0 3.41e-01 70.6% 91.9%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.55 39.0 2.74e-01 75.3% 88.4%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.55 38.0 3.58e-01 71.8% 95.2%
3fy6A01 3.30.2210.10 Alpha Beta › 2-Layer Sandwich › Integron cassette protein fold › Integron cassette protein superfamily 0.53 37.0 3.51e-01 74.1% 72.9%
3ce9A02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.52 43.0 3.35e-01 91.8% 89.2%
4dhiB02 1.20.1300.20 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Peptidase C65 Otubain, subdomain 2 0.52 37.0 3.11e-01 98.8% 44.1%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3386642 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.67 51.0 4.97e-01 82.4% 73.7%
3971939 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.66 50.0 5.05e-01 100.0% 81.2%
3067828 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.64 47.0 4.92e-01 82.4% 85.9%
4449599 148.1.3.47 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DNAX_ATPase_lid 0.64 44.0 4.75e-01 98.8% 87.1%
3946728 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.63 44.0 4.22e-01 72.9% 82.0%
3709879 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.63 45.0 4.71e-01 75.3% 88.0%
55657 162.1.1.0 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD 0.63 45.0 4.46e-01 75.3% 93.3%
4274766 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.62 46.0 4.29e-01 82.4% 63.8%
3235832 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.61 46.0 2.99e-01 80.0% 39.5%
3394467 142.3.1.0 ↗ alpha complex topology › Sigma2 domain-like › Mitochondrial morphogenesis protein Sld7 C-terminal domain › Mitochondrial morphogenesis protein Sld7 C-terminal domain 0.60 52.0 5.16e-01 98.8% 97.8%
3226186 101.1.10.4 ↗ alpha arrays › HTH › HTH › Cyclin-like › RB_B 0.60 54.0 4.28e-01 100.0% 83.5%
4515252 2007.1.18.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) › MTD 0.59 50.0 3.59e-01 95.3% 64.1%
56928 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.59 42.0 3.81e-01 74.1% 87.8%
5069175 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.58 39.0 4.04e-01 72.9% 72.5%
3910956 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.57 41.0 2.99e-01 77.6% 53.5%
3597328 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.57 46.0 4.59e-01 92.9% 93.3%
3740646 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.56 39.0 4.01e-01 71.8% 82.5%
5060017 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.55 36.0 3.98e-01 72.9% 86.2%
4935665 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.53 38.0 3.90e-01 72.9% 90.0%
3222449 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.53 42.0 2.94e-01 88.2% 51.5%
5012658 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.53 37.0 3.65e-01 72.9% 80.0%
3413073 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.53 35.0 3.22e-01 72.9% 49.2%
4146104 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.52 37.0 3.72e-01 74.1% 75.3%
3898611 611.12.1.1 ↗ alpha bundles › N-cbl like › Izumo sperm-egg fusion protein 1 N-terminal domain › Izumo sperm-egg fusion protein 1 N-terminal domain › IZUMO 0.51 41.0 3.69e-01 91.8% 80.0%
3590073 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.51 40.0 4.02e-01 82.4% 85.9%
4464616 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.50 35.0 3.45e-01 71.8% 73.3%
D2 high residues 108-239
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03837.20 best RecT 52.7 5.80e-14 99.2% 48.7%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1azpA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 21.0 2.95e-01 87.9% 59.1%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 23.0 3.60e-01 97.7% 91.8%
1fr3A00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.54 23.0 3.05e-01 97.7% 71.6%
1lomA00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.53 22.0 2.53e-01 89.4% 44.6%
3k1lA01 3.30.457.40 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.53 29.0 3.29e-01 96.2% 70.7%
2pn5A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.52 27.0 3.17e-01 78.8% 69.8%
2byvE05 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 22.0 2.74e-01 78.0% 60.8%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3862816 391.1.2.1 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › VWC 0.58 27.0 3.59e-01 91.7% 84.4%
4476789 3124.1.1.1 ↗ beta sandwiches › Nascent polypeptide-associated complex (NAC) dimerization domain › Nascent polypeptide-associated complex (NAC) dimerization domain › Nascent polypeptide-associated complex (NAC) dimerization domain › NAC 0.54 21.0 3.19e-01 75.0% 83.6%
3217960 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.52 39.0 4.28e-01 97.0% 99.0%