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NC_025470.1__YP_009104218.1__S140_220__00217

Bact-Vir

NC_025470.1__YP_009104218.1__S140_220__00217

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

92.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

Singleton — not in a non-trivial cluster

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 medium residues 5-57_121-131
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1bqbA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.62 54.0 4.21e-01 100.0% 92.4%
2dpmA02 1.10.1020.10 Mainly Alpha › Orthogonal Bundle › Adenine-specific Methyltransferase; domain 2 › Adenine-specific Methyltransferase, Domain 2 0.56 42.0 3.69e-01 92.2% 51.5%
2qhoD00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.54 34.0 3.72e-01 93.8% 77.6%
2jarA02 1.10.40.40 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Deoxyribonucleotidase; domain 2 0.51 39.0 4.14e-01 100.0% 96.4%
2ip2A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 35.0 2.47e-01 75.0% 22.4%
3lcvB01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.50 37.0 3.93e-01 93.8% 91.2%
2r6aC01 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.50 36.0 3.21e-01 76.6% 76.0%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3278996 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.53 40.0 3.54e-01 84.4% 53.0%
D2 medium residues 58-120
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fxxB01 6.10.140.1790 Special › Helix non-globular › Helix Hairpins › 0.62 40.0 3.85e-01 93.7% 58.3%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.62 46.0 4.10e-01 81.0% 63.7%
3terA00 1.10.287.3550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 38.0 2.99e-01 76.2% 33.6%
1uruA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.59 44.0 3.16e-01 82.5% 81.8%
5a4uF02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 40.0 3.28e-01 74.6% 86.8%
1rw1A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.57 42.0 3.57e-01 90.5% 45.6%
1v4aA01 1.10.4050.10 Mainly Alpha › Orthogonal Bundle › Nucleotidyltransferase substrate binding subunit/domain fold › Glutamine synthase adenylyltransferase GlnE 0.56 38.0 3.21e-01 81.0% 40.4%
3rgoA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.56 35.0 2.61e-01 81.0% 26.1%
4nn5A00 1.20.1250.90 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Thymic stromal lymphopoietin 0.56 41.0 3.38e-01 77.8% 79.8%
5uagE00 3.90.940.10 Alpha Beta › Alpha-Beta Complex › Eukaryotic RPB6 RNA polymerase subunit › RNA polymerase subunit, RPB6/omega 0.55 42.0 3.82e-01 96.8% 59.6%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 38.0 3.20e-01 74.6% 92.4%
2pg0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.55 41.0 3.22e-01 84.1% 63.8%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.53 36.0 2.89e-01 96.8% 38.9%
4g6dB02 6.10.140.1800 Special › Helix non-globular › Helix Hairpins › 0.52 34.0 3.23e-01 74.6% 53.1%
3gzfD00 1.10.150.420 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Coronavirus nonstructural protein 4 C-terminus 0.52 43.0 3.85e-01 92.1% 76.9%
1c6rA00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.51 43.0 3.85e-01 92.1% 98.9%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.51 36.0 2.97e-01 73.0% 81.3%
2qgaB03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.51 35.0 3.54e-01 76.2% 77.3%
2oqmB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.51 39.0 2.99e-01 88.9% 56.8%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3436766 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.64 46.0 3.71e-01 77.8% 77.6%
4010451 3788.1.1.15 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › PF27202 0.61 44.0 4.22e-01 77.8% 82.7%
3429164 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 43.0 3.76e-01 77.8% 82.1%
3178786 7579.1.1.44 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_6 0.58 45.0 2.91e-01 84.1% 85.9%
3986190 110.1.1.0 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.57 47.0 4.28e-01 100.0% 80.6%
3719527 2486.1.1.11 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_2 0.56 46.0 2.70e-01 93.7% 46.1%
3539251 633.24.1.4 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › RIN1 0.56 35.0 2.93e-01 100.0% 39.0%
3696555 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.55 39.0 2.94e-01 77.8% 71.4%
3270116 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.55 40.0 3.51e-01 77.8% 97.9%
4014978 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 45.0 3.97e-01 92.1% 62.2%
3359538 109.4.1.1261 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_long 0.54 43.0 3.25e-01 93.7% 39.4%
3718689 101.1.2.392 ↗ alpha arrays › HTH › HTH › winged helix domain › SNRNP200_wHTH 0.53 45.0 3.37e-01 90.5% 40.0%
4484502 107.1.1.9 ↗ alpha arrays › Cytochrome c-like › Cytochrome c › Cytochrome c › Cytochrome_CBB3 0.52 42.0 3.81e-01 88.9% 100.0%