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NC_019925.1__YP_007237445.1__G379_gp016__00123

Bact-Vir

NC_019925.1__YP_007237445.1__G379_gp016__00123

Identity

Accession:
NC_019925 ↗
Kingdom:
phage

Quality

88.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Limestonevirus› Dickeya_phage_vB-DsoM-LIMEstone1

TaxID: 2678590

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 8-88
PDB
Domain cluster: rep: MK327928.1__QBO60798.1__G2133_00059__00059__D10-93
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 34.0 4.37e-01 80.2% 81.4%
4rg9B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.64 41.0 3.21e-01 100.0% 31.1%
3x17A02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.62 47.0 2.94e-01 80.2% 100.0%
4ui9Y03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 41.0 4.13e-01 98.8% 67.5%
4j8dD00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 42.0 3.39e-01 74.1% 86.4%
1hr5A00 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 0.60 35.0 4.37e-01 79.0% 100.0%
3aqlA02 1.10.3090.10 Mainly Alpha › Orthogonal Bundle › cca-adding enzyme, domain 2 › cca-adding enzyme, domain 2 0.60 54.0 3.77e-01 98.8% 56.9%
1dq3A02 3.30.160.90 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 40.0 4.15e-01 71.6% 100.0%
2gz6A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.58 44.0 2.88e-01 82.7% 96.0%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 41.0 4.04e-01 93.8% 70.6%
3h7lB02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.56 45.0 2.72e-01 85.2% 46.5%
2py6A01 1.20.1270.160 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.56 32.0 3.34e-01 97.5% 57.5%
3rkoG00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 43.0 4.06e-01 100.0% 69.0%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 39.0 2.90e-01 77.8% 38.3%
8h1kA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.54 43.0 2.74e-01 86.4% 52.5%
3gt5A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.53 43.0 2.77e-01 88.9% 51.4%
2n1fA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.52 39.0 3.82e-01 92.6% 73.0%
8bykA01 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.52 43.0 2.82e-01 97.5% 96.8%
5gxxA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.52 44.0 2.77e-01 93.8% 54.1%
2afaA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 41.0 2.64e-01 88.9% 49.3%
4v1sA00 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 40.0 2.64e-01 86.4% 44.6%
3t33A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.50 40.0 2.60e-01 88.9% 41.3%
3r07C00 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.50 36.0 3.58e-01 76.5% 72.7%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3675872 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 0.76 38.0 3.26e-01 79.0% 32.8%
3982704 2484.1.1.115 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_IS66 0.59 38.0 3.12e-01 84.0% 37.9%
3525931 109.4.1.1421 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_8, TPR_19 0.57 39.0 3.16e-01 100.0% 35.2%
3645176 3599.1.1.1 ↗ alpha superhelices › Mitochondrial malonyl-CoA decarboxylase helical domain › Mitochondrial malonyl-CoA decarboxylase helical domain › Mitochondrial malonyl-CoA decarboxylase helical domain › MCD_N 0.55 41.0 3.28e-01 77.8% 83.9%
3727368 609.1.1.0 ↗ alpha bundles › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase 0.55 42.0 3.41e-01 80.2% 83.3%
3088550 109.2.1.22 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid › GlcNAc_2-epim 0.55 45.0 2.82e-01 87.7% 53.0%
5828 330.7.1.3 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › Stirrup 0.55 40.0 4.10e-01 76.5% 100.0%
3932343 109.4.1.2532 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2, TPR_6, TPR_8, TPR_16, TPR_19 0.55 38.0 2.45e-01 87.7% 15.9%
3856774 110.1.1.18 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain › Death_Lrrd1 0.54 39.0 3.30e-01 79.0% 93.5%
3621619 2006.1.4.9 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › RNase_Zc3h12a 0.53 47.0 3.38e-01 98.8% 66.3%
4045999 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.53 44.0 3.42e-01 97.5% 75.0%
4951992 5041.1.1.55 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › DUF1622 0.53 47.0 4.44e-01 100.0% 94.0%
3589835 5069.1.3.26 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF1622 0.52 46.0 4.16e-01 98.8% 85.5%
4681219 3681.1.1.0 ↗ a+b complex topology › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit 0.52 39.0 3.51e-01 81.5% 62.6%
5021813 5058.1.1.101 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › DUF1622 0.51 46.0 4.20e-01 100.0% 89.5%
4978720 109.2.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.51 41.0 2.74e-01 88.9% 57.3%
4488200 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.50 34.0 3.12e-01 81.5% 52.3%
D2 medium residues 148-289
PDB
Domain cluster: representative