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NC_019925.1__YP_007237515.1__G379_gp039__00193

Bact-Vir

NC_019925.1__YP_007237515.1__G379_gp039__00193

Identity

Accession:
NC_019925 ↗
Kingdom:
phage

Quality

93.1 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 5-63
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6wshA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.76 56.0 5.78e-01 76.3% 94.5%
1s8nA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.75 53.0 5.42e-01 74.6% 91.4%
4ii2A02 3.40.50.12550 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 0.75 67.0 4.52e-01 100.0% 30.0%
2ahoB02 1.10.150.190 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 0.73 54.0 4.64e-01 78.0% 87.9%
2bg1A01 3.90.1310.40 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › 0.72 51.0 4.66e-01 74.6% 75.3%
3e3vA03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.70 57.0 5.88e-01 98.3% 98.2%
3ousA00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 57.0 5.11e-01 91.5% 86.6%
3dfgA03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 50.0 5.38e-01 91.5% 100.0%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 56.0 4.90e-01 91.5% 81.6%
4g6dB02 6.10.140.1800 Special › Helix non-globular › Helix Hairpins › 0.66 52.0 4.72e-01 86.4% 75.3%
2p5tA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.66 46.0 4.01e-01 100.0% 47.8%
3d5lA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 46.0 5.09e-01 98.3% 100.0%
6rv2A00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 57.0 3.73e-01 100.0% 47.2%
1z21A00 1.10.10.1000 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Type III secretion system virulence factor YopR, core domain 0.58 48.0 4.22e-01 100.0% 61.5%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.57 43.0 4.08e-01 93.2% 67.6%
2doeA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.56 45.0 4.19e-01 100.0% 68.7%
2xvtC00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.56 48.0 4.44e-01 100.0% 86.1%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.55 46.0 4.48e-01 96.6% 92.5%
3f2eA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 46.0 4.23e-01 100.0% 74.7%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.55 47.0 4.32e-01 100.0% 76.5%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.54 43.0 3.74e-01 86.4% 96.6%
4hwdD00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.53 47.0 4.09e-01 100.0% 77.8%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 44.0 4.01e-01 98.3% 71.4%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.51 44.0 3.55e-01 100.0% 91.5%
2a0bA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.51 42.0 3.50e-01 100.0% 67.8%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4093240 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.79 63.0 6.49e-01 100.0% 94.5%
3287744 103.12.1.1 ↗ alpha arrays › RuvA-C › ANTAR domain › ANTAR domain › ANTAR 0.77 57.0 5.75e-01 78.0% 88.3%
4452388 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.76 59.0 6.24e-01 98.3% 100.0%
1870443 6076.1.1.2 ↗ alpha arrays › Catalytic cysteine domain in ubiquitin-activating enzyme › Catalytic cysteine domain in ubiquitin-activating enzyme › Catalytic cysteine domain in ubiquitin-activating enzyme › E1_4HB 0.76 68.0 6.39e-01 100.0% 95.8%
4254949 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.71 52.0 5.37e-01 98.3% 85.5%
4119329 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.70 53.0 5.47e-01 100.0% 89.1%
3269933 101.1.1.67 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-bind_6 0.70 60.0 5.71e-01 96.6% 85.7%
2808686 103.12.1.1 ↗ alpha arrays › RuvA-C › ANTAR domain › ANTAR domain › ANTAR 0.70 50.0 4.93e-01 76.3% 79.7%
5027329 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.66 58.0 5.42e-01 100.0% 86.7%
3251975 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.64 54.0 5.19e-01 100.0% 88.6%
3936168 2484.1.1.104 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_1 0.64 46.0 3.59e-01 79.7% 34.3%
3510771 610.4.1.0 ↗ alpha arrays › ERP29 C domain-like › YqeY domain › YqeY domain 0.63 52.0 4.51e-01 96.6% 58.0%
4874187 3051.1.1.1 ↗ alpha arrays › Superantigen MAM C-terminal domain › Superantigen MAM C-terminal domain › Superantigen MAM C-terminal domain › MA-Mit 0.61 44.0 3.45e-01 76.3% 54.6%
3507860 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 46.0 4.00e-01 91.5% 54.3%
3971758 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.54 43.0 3.82e-01 93.2% 60.0%
4026045 101.1.4.85 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3, PF28877 0.52 37.0 3.72e-01 76.3% 96.7%
4525341 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.52 44.0 4.19e-01 93.2% 92.9%
3974625 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.51 44.0 4.18e-01 93.2% 92.9%