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NC_055800.1__YP_010102565.1__KNU58_gp140__00125

Bact-Vir

NC_055800.1__YP_010102565.1__KNU58_gp140__00125

Identity

Accession:
NC_055800 ↗
Kingdom:
phage

Quality

83.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Demerecviridae› Thalassavirus› Vibrio_phage_Brizo

TaxID: 2590896

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 high residues 14-107
PDB
Domain cluster: rep: MW824421.1__QZI92852.1__SIPHO067v1_p0012__00012__D1-71
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4a17U01 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 49.0 5.41e-01 88.3% 81.8%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.66 46.0 4.35e-01 88.3% 60.7%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.65 54.0 4.39e-01 89.4% 73.4%
6g94A00 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.64 45.0 3.71e-01 80.9% 40.7%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.62 48.0 4.04e-01 81.9% 50.3%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.61 51.0 3.94e-01 90.4% 76.8%
1ivhA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.60 37.0 3.28e-01 80.9% 41.1%
5nl6B01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 52.0 4.74e-01 91.5% 79.3%
7wz5A01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.60 49.0 4.22e-01 90.4% 80.8%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.59 42.0 4.44e-01 96.8% 83.1%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 51.0 4.75e-01 91.5% 82.1%
1t72A01 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 0.58 49.0 4.57e-01 91.5% 73.5%
6yz2A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.58 47.0 4.36e-01 94.7% 69.2%
6vydA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 47.0 3.32e-01 90.4% 32.9%
6wh0A01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.56 43.0 3.70e-01 100.0% 50.7%
1siqA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.56 44.0 3.73e-01 85.1% 94.2%
3acxA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 40.0 2.93e-01 88.3% 26.1%
1rx0A03 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 42.0 3.52e-01 90.4% 48.4%
2fji101 1.10.357.50 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.54 48.0 3.75e-01 100.0% 73.7%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.53 41.0 3.67e-01 97.9% 60.3%
3hq2B00 1.10.1370.30 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › 0.52 43.0 2.70e-01 90.4% 93.2%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 42.0 3.79e-01 90.4% 82.1%
8cdaB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.51 43.0 3.61e-01 92.6% 56.0%
3wvoC02 1.10.132.100 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.50 35.0 3.21e-01 72.3% 80.0%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5015832 615.1.1.0 ↗ alpha arrays › T4 endonuclease V › T4 endonuclease V › T4 endonuclease V 0.93 86.0 7.31e-01 100.0% 65.2%
3272466 615.1.1.1 ↗ alpha arrays › T4 endonuclease V › T4 endonuclease V › T4 endonuclease V › Pyr_excise 0.89 85.0 7.55e-01 100.0% 76.0%
5040981 615.1.1.0 ↗ alpha arrays › T4 endonuclease V › T4 endonuclease V › T4 endonuclease V 0.89 82.0 6.66e-01 100.0% 56.9%
3759004 622.1.1.22 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › TF_AP-2 0.70 47.0 4.30e-01 80.9% 52.0%
4522619 5051.1.1.0 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like 0.67 51.0 3.31e-01 80.9% 70.5%
5001397 316.1.1.41 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF6036 0.64 45.0 3.45e-01 100.0% 33.2%
3742375 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.62 52.0 4.53e-01 91.5% 79.3%
3998932 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 56.0 4.54e-01 97.9% 80.6%
3350203 3652.1.1.5 ↗ alpha duplicates or obligate multimers › Qua1 › Qua1 › Qua1 › SF1-HH 0.60 50.0 5.22e-01 90.4% 95.3%
4930774 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.59 47.0 4.14e-01 90.4% 58.3%
3276208 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.59 55.0 3.33e-01 100.0% 28.2%
3843567 3554.1.1.4 ↗ a+b duplicates or obligate multimers › protein of unknown function (eca1910) › protein of unknown function (eca1910) › protein of unknown function (eca1910) › TF_AP-2 0.58 47.0 4.37e-01 87.2% 81.7%
3796044 633.21.1.10 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › MARVEL 0.58 50.0 4.14e-01 91.5% 56.9%
3254127 633.6.1.8 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX_C_alpha1 0.57 44.0 3.51e-01 80.9% 78.9%
3417339 633.23.1.32 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › CASP_dom 0.57 47.0 3.86e-01 88.3% 92.7%
4068922 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.57 47.0 4.55e-01 88.3% 88.6%
4075008 633.21.1.18 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom 0.57 47.0 3.86e-01 88.3% 92.7%
3595979 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.56 43.0 4.34e-01 79.8% 78.9%
4954528 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.56 42.0 3.79e-01 80.9% 57.7%
3442938 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 49.0 3.33e-01 100.0% 48.2%
3710128 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.54 45.0 3.27e-01 90.4% 77.6%
3264751 4044.1.1.0 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins 0.53 40.0 3.44e-01 78.7% 72.4%
3690657 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.53 42.0 3.69e-01 85.1% 72.9%
3733469 375.1.1.26 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 0.52 44.0 3.83e-01 91.5% 86.2%
3237990 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.51 43.0 3.44e-01 93.6% 47.7%
3214333 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.51 44.0 4.14e-01 94.7% 79.1%
3655694 4992.1.1.0 ↗ extended segments › RelB-like › RelB-like › RelB-like 0.51 39.0 4.09e-01 80.9% 89.4%
3713349 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.51 45.0 3.45e-01 100.0% 43.3%
4303493 3016.1.1.10 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › GDC-P 0.51 28.0 2.94e-01 100.0% 57.6%
3374157 2484.1.1.157 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.50 39.0 2.51e-01 86.2% 28.3%
D2 high residues 132-245
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o38A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.59 29.0 3.60e-01 77.2% 78.5%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4530543 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.68 34.0 4.34e-01 76.3% 80.0%
3267839 577.1.1.1 ↗ alpha arrays › CRIB domain › CRIB domain › CRIB domain › PBD 0.54 27.0 3.33e-01 79.8% 79.1%
D3 high residues 263-348
PDB
Domain cluster: rep: OQ362005.1__WCX68730.1__X__00105__D12-94
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kjmB01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.55 34.0 3.84e-01 73.3% 84.1%
3k7dA01 1.20.120.1510 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.55 41.0 3.79e-01 81.4% 76.1%
2mx8A01 1.10.274.70 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain 0.54 45.0 4.14e-01 90.7% 75.2%
3gn3A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 44.0 3.55e-01 95.3% 74.3%
5g5gA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.52 44.0 4.44e-01 97.7% 92.2%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.52 41.0 3.55e-01 87.2% 63.0%
2xseA00 1.20.120.1440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain 0.52 40.0 3.33e-01 84.9% 62.9%
4kc9A02 1.20.120.1750 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 40.0 3.03e-01 86.0% 51.6%
1aisB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.51 41.0 3.97e-01 88.4% 82.8%
1el4A00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.50 42.0 3.25e-01 91.9% 80.4%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3586184 5059.1.1.5 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › UAA 0.57 40.0 2.71e-01 73.3% 60.3%
3942472 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.53 45.0 3.65e-01 95.3% 76.0%
3175429 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.53 40.0 3.62e-01 82.6% 86.4%
3831462 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 38.0 2.89e-01 96.5% 29.6%
3970916 7108.1.1.1 ↗ alpha complex topology › Stl repressor, middle domain › Stl repressor, middle domain › Stl repressor, middle domain › DUF3418 0.52 37.0 3.79e-01 75.6% 80.0%
3714843 592.6.1.0 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain 0.52 41.0 3.96e-01 90.7% 76.0%
3588063 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.51 39.0 3.71e-01 81.4% 95.1%
3395683 386.1.1.19 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_2 0.51 38.0 3.54e-01 77.9% 74.3%
4169057 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.51 38.0 3.67e-01 79.1% 74.7%
3989723 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.50 33.0 3.73e-01 73.3% 89.2%