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NC_054438.1__YP_010051102.1__KDJ61_gp13__00013

Bact-Vir

NC_054438.1__YP_010051102.1__KDJ61_gp13__00013

Identity

Accession:
NC_054438 ↗
Kingdom:
phage

Quality

67.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vendettavirus› Gordonia_phage_TZGordon

TaxID: 2744004

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 2-33
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4p1mB01 3.30.160.880 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Cell division protein ZapA protomer, N-terminal domain 0.83 64.0 5.80e-01 87.5% 66.7%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.72 57.0 5.16e-01 100.0% 68.0%
2jl8102 3.30.160.850 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 49.0 4.66e-01 87.5% 66.7%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.67 49.0 4.39e-01 90.6% 54.5%
3u5wA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.67 54.0 3.71e-01 100.0% 40.5%
3tj8A02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.63 46.0 3.88e-01 96.9% 77.0%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.61 47.0 3.76e-01 100.0% 92.4%
2vfrA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.60 49.0 3.38e-01 100.0% 30.0%
1t95A01 3.30.1250.10 Alpha Beta › 2-Layer Sandwich › Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; › Ribosome maturation protein SBDS, N-terminal domain 0.59 43.0 3.61e-01 100.0% 100.0%
4h0aA00 3.40.33.10 Alpha Beta › 3-Layer(aba) Sandwich › Pathogenesis-related Protein p14a › CAP 0.59 43.0 2.56e-01 84.4% 18.5%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.59 46.0 3.76e-01 100.0% 57.9%
1ileA02 3.90.740.10 Alpha Beta › Alpha-Beta Complex › Isoleucyl-tRNA Synthetase; domain 2 › Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain 0.59 46.0 2.93e-01 100.0% 16.9%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 42.0 3.14e-01 87.5% 68.0%
4umwA02 2.70.150.10 Mainly Beta › Distorted Sandwich › Calcium-transporting ATPase, cytoplasmic transduction domain A › Calcium-transporting ATPase, cytoplasmic transduction domain A 0.58 49.0 3.65e-01 100.0% 36.0%
1xexB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 41.0 2.74e-01 87.5% 18.0%
2z86D02 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.56 39.0 2.33e-01 75.0% 7.7%
2x49A02 3.40.5.40 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › FHIPEP family, domain 2 0.56 41.0 3.82e-01 93.8% 100.0%
4dnhA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 43.0 2.51e-01 96.9% 99.0%
1g8mA02 3.40.140.20 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › AICAR transformylase, duplication domain 0.55 38.0 2.49e-01 78.1% 99.4%
2mp4A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 41.0 2.77e-01 100.0% 35.2%
2yhaA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 38.0 2.51e-01 100.0% 27.1%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 36.0 2.84e-01 100.0% 98.2%
4mzuF02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 40.0 2.78e-01 100.0% 23.0%
2rbkA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.52 36.0 2.75e-01 81.2% 83.2%
1nxmA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 39.0 2.53e-01 100.0% 18.0%
2r8rA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 40.0 2.47e-01 84.4% 29.7%
2mhyA00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.50 35.0 3.30e-01 100.0% 57.9%
1oi6A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.50 36.0 2.43e-01 100.0% 30.7%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
224284 857.1.1.1 ↗ a+b duplicates or obligate multimers › Cell division protein ZapA-like › Cell division protein ZapA-like › Cell division protein ZapA-like › ZapA 0.78 59.0 4.29e-01 87.5% 32.3%
4935498 304.135.1.0 ↗ a+b two layers › Alpha-beta plaits › O-phosphoseryl-tRNA synthetase C-terminal domain › O-phosphoseryl-tRNA synthetase C-terminal domain 0.73 56.0 3.49e-01 100.0% 15.6%
3281602 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.69 53.0 4.95e-01 100.0% 83.3%
4481010 857.1.1.1 ↗ a+b duplicates or obligate multimers › Cell division protein ZapA-like › Cell division protein ZapA-like › Cell division protein ZapA-like › ZapA 0.69 52.0 3.80e-01 87.5% 30.0%
4959407 304.163.1.3 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.68 54.0 4.90e-01 100.0% 80.0%
3946755 605.1.1.26 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF2058 0.66 48.0 3.45e-01 84.4% 40.9%
3754343 4.1.1.311 ↗ beta barrels › SH3 › SH3 › SH3 › BRWD_AD 0.66 53.0 4.23e-01 100.0% 72.0%
3959955 304.163.1.3 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.66 51.0 4.79e-01 100.0% 91.1%
3518601 389.1.1.0 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin 0.66 46.0 2.86e-01 75.0% 14.4%
3624854 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.66 55.0 4.03e-01 100.0% 37.9%
3371461 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.65 51.0 3.93e-01 100.0% 86.7%
None — 0.62 52.0 3.33e-01 100.0% 40.0%
3264411 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 46.0 3.70e-01 100.0% 86.3%
3970650 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 48.0 2.81e-01 87.5% 25.7%
3573877 136.1.1.3 ↗ alpha complex topology › Heme-dependent peroxidases › Heme-dependent peroxidases › Heme-dependent peroxidases › An_peroxidase 0.59 43.0 2.76e-01 93.8% 18.6%
3297110 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.59 47.0 3.31e-01 87.5% 28.0%
3961736 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.58 44.0 2.83e-01 84.4% 81.1%
3597792 221.7.1.0 ↗ a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 0.58 46.0 3.37e-01 100.0% 70.9%
5079277 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.57 41.0 3.62e-01 87.5% 48.3%
3519254 6171.1.1.0 ↗ 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 0.56 43.0 2.83e-01 100.0% 37.2%
3258276 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.56 41.0 2.64e-01 96.9% 30.2%
3301989 10.12.1.16 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › 2OG-FeII_Oxy 0.55 42.0 2.55e-01 100.0% 16.9%
3817222 221.1.1.1 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Fer2 0.55 40.0 3.23e-01 100.0% 68.5%
3578203 209.1.1.0 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.54 41.0 2.62e-01 81.2% 42.0%
4145964 247.1.1.29 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_2, Anti-Pycsar_Apyc1 0.54 40.0 2.38e-01 96.9% 7.9%
4047031 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.54 39.0 2.96e-01 100.0% 79.1%
2991657 7602.1.1.1 ↗ a/b three-layered sandwiches › Lactate racemase C-terminal domain › Lactate racemase C-terminal domain › Lactate racemase C-terminal domain › LarA_C 0.53 40.0 4.16e-01 87.5% 93.1%
4033892 3012.1.1.4 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Hydrolase_3 0.51 41.0 3.04e-01 100.0% 57.0%
4955560 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.51 38.0 3.33e-01 71.9% 45.5%
1117568 2003.1.2.9 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GDI 0.50 39.0 2.33e-01 96.9% 33.4%