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NC_019925.1__YP_007237404.1__G379_gp136__00082

Bact-Vir

NC_019925.1__YP_007237404.1__G379_gp136__00082

Identity

Accession:
NC_019925 ↗
Kingdom:
phage

Quality

64.3 mean pLDDT

Taxonomy

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

TaxID: 2678590

Cluster

View cluster (5 members)

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 6-119_151-158
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3oe3C00 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.58 34.0 3.84e-01 82.8% 77.3%
2g3aA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 42.0 4.55e-01 77.0% 97.1%
2p18A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 44.0 3.37e-01 82.0% 49.8%
1uasA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 31.0 3.53e-01 77.9% 73.9%
4a1nA01 3.40.570.10 Alpha Beta › 3-Layer(aba) Sandwich › Extracellular Endonuclease; Chain A › Extracellular Endonuclease, subunit A 0.55 41.0 3.28e-01 77.9% 85.0%
3n4eA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 32.0 3.43e-01 73.0% 67.3%
2gu3A01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 29.0 3.88e-01 81.1% 100.0%
4ifdE00 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.53 42.0 3.32e-01 86.1% 73.8%
1jyaB00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 38.0 3.89e-01 76.2% 89.3%
4xrtA02 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 37.0 3.44e-01 74.6% 62.5%
2z4hA01 2.40.128.300 Mainly Beta › Beta Barrel › Lipocalin › NlpE, N-terminal domain 0.52 29.0 3.43e-01 77.0% 82.3%
3gkeA02 3.90.380.10 Alpha Beta › Alpha-Beta Complex › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 0.51 41.0 3.45e-01 86.1% 90.0%
3ijtB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 40.0 3.79e-01 92.6% 69.9%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2485676 292.3.1.1 ↗ a+b two layers › RIP/Polo-box domain › TipC soluble domain › TipC soluble domain › TipC 0.71 54.0 4.70e-01 78.7% 68.7%
3536489 331.9.1.5 ↗ a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain › AP4E_app_platf 0.67 35.0 3.77e-01 85.2% 58.1%
3624850 331.9.1.9 ↗ a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain › PF26171 0.65 35.0 3.78e-01 86.1% 60.0%
3887495 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.63 36.0 3.73e-01 71.3% 58.3%
5004406 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.62 49.0 4.64e-01 84.4% 85.5%
3936785 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.61 32.0 3.48e-01 84.4% 59.0%
3214007 145.1.1.1 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box 0.60 41.0 4.14e-01 77.9% 68.0%
3420866 216.1.1.9 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › FANCL_d2 0.59 32.0 3.49e-01 86.9% 63.0%
3204895 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.59 41.0 3.94e-01 70.5% 96.4%
3589569 243.3.1.13 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF5590 0.55 28.0 3.89e-01 79.5% 100.0%
4153442 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 41.0 4.18e-01 85.2% 79.2%
3506274 331.2.1.7 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM1_C_vert_fung 0.54 38.0 3.80e-01 83.6% 69.6%
4020163 216.1.1.1 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UQ_con 0.54 34.0 3.17e-01 85.2% 50.0%
3388825 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.54 32.0 3.56e-01 77.0% 76.7%
3996796 12.5.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related 0.52 40.0 3.75e-01 82.0% 96.1%
3962288 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.52 38.0 3.73e-01 74.6% 73.1%
3398140 4.1.1.326 ↗ beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.51 29.0 3.64e-01 77.0% 92.0%
370870 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.51 40.0 3.85e-01 92.6% 73.0%
3638899 5.1.4.78 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › TFIIIC_delta 0.51 37.0 2.41e-01 75.4% 97.8%
3252050 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.51 42.0 3.52e-01 90.2% 65.7%
3408388 4.1.1.326 ↗ beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.51 30.0 3.57e-01 77.0% 88.7%
3583345 5.1.4.288 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › APEH_N 0.50 37.0 2.58e-01 78.7% 92.5%