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NC_048077.1__YP_009813563.1__HOU32_gp118__00118

Bact-Vir

NC_048077.1__YP_009813563.1__HOU32_gp118__00118

Identity

Accession:
NC_048077 ↗
Kingdom:
phage

Quality

89.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Salmondvirus› Dickeya_phage_vB_DsoM_JA11

TaxID: 2382310

Cluster

View cluster (40 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 223-277
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fp1B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.80 60.0 4.15e-01 96.4% 26.2%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.79 61.0 4.74e-01 81.8% 50.5%
4qdjA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.79 49.0 3.18e-01 80.0% 16.8%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.75 49.0 3.72e-01 72.7% 28.7%
1bh9B00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.75 61.0 5.17e-01 96.4% 55.1%
3vkgA11 1.20.920.20 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.74 56.0 4.43e-01 96.4% 40.9%
2qpvA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.72 54.0 4.02e-01 80.0% 97.7%
1xl3C00 1.20.1280.80 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.72 55.0 4.60e-01 81.8% 52.7%
7egfc01 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.70 62.0 5.29e-01 98.2% 62.8%
3ff5A00 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 35.0 3.60e-01 78.2% 50.0%
3s5tA01 3.30.565.40 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Fervidobacterium nodosum Rt17-B1 like 0.69 52.0 3.77e-01 100.0% 29.4%
3t6pA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.69 55.0 5.23e-01 89.1% 83.3%
3b0cW00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.69 57.0 5.21e-01 98.2% 69.9%
3rkgA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.67 60.0 4.14e-01 94.5% 36.6%
1e6cA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 47.0 3.34e-01 78.2% 24.1%
3n71A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 60.0 3.99e-01 100.0% 42.7%
6czfA01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.66 45.0 2.84e-01 76.4% 12.5%
2lo6A00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.66 46.0 3.33e-01 72.7% 26.6%
1af7A01 1.10.155.10 Mainly Alpha › Orthogonal Bundle › Chemotaxis Receptor Methyltransferase Cher; domain 1 › Chemotaxis receptor methyltransferase CheR, N-terminal domain 0.65 47.0 4.11e-01 76.4% 72.5%
1ze0A02 1.10.4070.10 Mainly Alpha › Orthogonal Bundle › putative redox-enzyme maturation protein fold › putative redox-enzyme maturation protein domain 0.64 44.0 3.98e-01 78.2% 51.3%
3lyeA00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.63 51.0 3.22e-01 89.1% 81.1%
2nn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.63 49.0 3.50e-01 85.5% 77.2%
2wh5A00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.62 47.0 3.95e-01 80.0% 92.2%
2dk4A00 4.10.280.110 Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Pre-mRNA processing factor 4 domain 0.62 45.0 4.13e-01 80.0% 57.9%
3otgA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.62 49.0 3.30e-01 90.9% 23.2%
1sw2A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.59 42.0 3.04e-01 78.2% 61.4%
1d8cA02 2.170.170.11 Mainly Beta › Beta Complex › Malate synthase G - maily-beta sub-domain › Malate synthase G - maily-beta sub-domain 0.58 47.0 3.62e-01 89.1% 60.9%
4k3bA04 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.56 43.0 3.92e-01 87.3% 66.7%
3u48A02 3.40.50.1700 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycoside hydrolase family 3 C-terminal domain 0.55 38.0 2.41e-01 70.9% 32.7%
2aj4B03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.55 41.0 3.03e-01 83.6% 28.4%
3i5tA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 42.0 2.66e-01 83.6% 24.5%
6v88A00 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.54 40.0 3.06e-01 78.2% 48.3%
3c7jA01 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 0.52 37.0 3.09e-01 72.7% 85.7%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4850945 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.80 63.0 3.86e-01 83.6% 91.3%
5000698 604.38.1.0 ↗ alpha bundles › Spectrin repeat-like › Legionella effector SdeA 3-helical bundle › Legionella effector SdeA 3-helical bundle 0.80 57.0 4.55e-01 74.5% 39.0%
3799526 5001.1.1.3 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_2 0.80 62.0 3.76e-01 81.8% 16.8%
3503293 109.4.1.470 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › INTS2 0.79 63.0 3.91e-01 90.9% 16.5%
3375068 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.78 56.0 4.19e-01 74.5% 32.8%
3836893 148.1.1.12 ↗ alpha arrays › Histone-like › Histone-related › Histone › Bromo_TP 0.77 66.0 5.75e-01 96.4% 63.7%
3405944 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.75 62.0 5.53e-01 96.4% 65.3%
3976839 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.75 55.0 4.47e-01 78.2% 51.0%
3619546 3712.1.1.0 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 0.74 60.0 5.69e-01 94.5% 73.8%
3298325 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.74 48.0 5.23e-01 70.9% 82.2%
3925064 148.1.1.7 ↗ alpha arrays › Histone-like › Histone-related › Histone › TAF 0.73 61.0 5.42e-01 96.4% 65.3%
3759368 544.1.1.4 ↗ alpha bundles › Functional domain of the splicing factor Prp18 › Functional domain of the splicing factor Prp18 › Functional domain of the splicing factor Prp18 › PF28319 0.73 53.0 4.25e-01 76.4% 65.7%
3638356 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.72 64.0 5.60e-01 98.2% 67.5%
3740452 148.1.1.4 ↗ alpha arrays › Histone-like › Histone-related › Histone › CBFD_NFYB_HMF 0.72 59.0 5.39e-01 98.2% 68.5%
3974803 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.71 62.0 4.19e-01 96.4% 28.3%
3809086 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.70 51.0 4.37e-01 80.0% 49.4%
3593162 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.69 55.0 3.29e-01 89.1% 13.1%
5073927 2004.1.1.196 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_22 0.69 48.0 3.31e-01 74.5% 22.6%
3725517 148.1.1.9 ↗ alpha arrays › Histone-like › Histone-related › Histone › TFIID_20kDa 0.68 59.0 5.23e-01 96.4% 66.3%
3426161 601.1.2.74 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Rx_N 0.67 58.0 4.27e-01 90.9% 71.5%
4096162 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.67 52.0 4.19e-01 81.8% 46.0%
4682031 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.66 58.0 3.29e-01 100.0% 13.5%
3934989 193.1.1.0 ↗ alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like 0.64 46.0 3.72e-01 78.2% 93.6%
5083838 3896.1.1.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase 0.63 49.0 3.28e-01 85.5% 23.4%
4821042 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.63 47.0 3.63e-01 83.6% 39.1%
4066690 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.62 43.0 3.58e-01 78.2% 40.0%
3811948 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.62 47.0 4.34e-01 81.8% 97.1%
4976543 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 47.0 3.45e-01 94.5% 29.1%
4011712 148.1.3.15 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_assoc_2 0.57 46.0 3.88e-01 89.1% 64.2%
3482984 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.53 44.0 2.98e-01 96.4% 87.4%
D2 medium residues 2-70
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4g09A03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 34.0 3.81e-01 75.4% 58.2%
3lcvB02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 46.0 3.29e-01 75.4% 54.5%
3mzkB03 1.20.58.940 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 42.0 4.27e-01 73.9% 81.4%
3ltoA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.60 46.0 3.68e-01 82.6% 82.8%
3htmA02 6.10.250.3030 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.59 34.0 4.21e-01 92.8% 100.0%
3gwrB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 40.0 3.28e-01 72.5% 91.3%
4b89A00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.57 46.0 3.23e-01 89.9% 39.1%
1h72C02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.55 44.0 3.56e-01 88.4% 64.4%
1crnA00 3.30.1350.10 Alpha Beta › 2-Layer Sandwich › Crambin › Thionin-like 0.54 33.0 3.80e-01 78.3% 93.5%
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.51 44.0 3.57e-01 97.1% 65.7%
6dxwA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.50 36.0 2.63e-01 79.7% 95.2%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3968135 2003.1.1.141 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Polysacc_synt_2, GDP_Man_Dehyd 0.65 49.0 3.07e-01 81.2% 58.2%
4986584 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.64 39.0 3.40e-01 76.8% 43.0%
3187315 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.60 43.0 2.91e-01 73.9% 33.9%
3695060 3431.1.1.1 ↗ alpha bundles › Helical domain in autophagy protein 5 › Helical domain in autophagy protein 5 › Helical domain in autophagy protein 5 › ATG5_HBR 0.59 38.0 3.92e-01 71.0% 69.2%
3835731 365.1.1.1 ↗ few secondary structure elements › Crambin-like › Crambin-like › Crambin-like › Thionin 0.59 34.0 3.88e-01 76.8% 84.4%
3408063 6039.1.1.1 ↗ few secondary structure elements › CLIP domain › CLIP domain › CLIP domain › CLIP 0.58 35.0 3.69e-01 75.4% 66.7%
1869443 226.1.1.2 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › Skp1 0.55 35.0 3.50e-01 72.5% 64.3%
1869442 226.1.1.2 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › Skp1 0.54 34.0 3.84e-01 73.9% 84.6%
4927168 2006.1.4.19 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N 0.54 39.0 2.76e-01 76.8% 75.0%
5055638 2006.1.4.19 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N 0.54 38.0 2.74e-01 75.4% 78.1%
5079552 2005.1.1.2 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1b 0.53 47.0 2.95e-01 100.0% 67.0%
3652480 109.2.1.14 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid › DUF608 0.53 42.0 2.55e-01 91.3% 39.1%
4972841 205.1.1.16 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_7 0.53 39.0 3.54e-01 82.6% 67.0%