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NC_048077.1__YP_009813719.1__HOU32_gp274__00274

Bact-Vir

NC_048077.1__YP_009813719.1__HOU32_gp274__00274

Identity

Accession:
NC_048077 ↗
Kingdom:
phage

Quality

80.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Salmondvirus› Dickeya_phage_vB_DsoM_JA11

TaxID: 2382310

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 1-57
PDB
D2 high residues 73-129
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7s03A01 1.10.10.1450 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.84 60.0 6.38e-01 80.7% 86.0%
1k78I00 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 0.81 63.0 6.30e-01 82.5% 84.5%
2q0oA02 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 0.73 48.0 4.60e-01 82.5% 58.2%
6dnwA01 3.90.1750.20 Alpha Beta › Alpha-Beta Complex › Hect, E3 ligase catalytic domain fold › Putative Large Serine Recombinase; Chain B, Domain 2 0.73 54.0 4.23e-01 84.2% 37.4%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.72 55.0 3.97e-01 86.0% 47.7%
4iejA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.71 53.0 4.88e-01 84.2% 61.3%
4ragA02 1.10.10.430 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Phosphatase 2C, C-terminal domain suprefamily 0.70 54.0 5.14e-01 84.2% 77.9%
1q8cA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.68 58.0 4.50e-01 98.2% 94.7%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.67 50.0 4.53e-01 84.2% 59.0%
3pvlA03 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.63 51.0 4.24e-01 100.0% 61.9%
2afbB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.62 43.0 2.65e-01 71.9% 80.4%
3i5pA03 1.20.120.1880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleoporin, helical C-terminal domain 0.61 51.0 3.46e-01 100.0% 63.1%
3bqoA00 1.25.40.210 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Telomere repeat-binding factor, dimerisation domain 0.61 50.0 3.58e-01 100.0% 39.6%
4fqnC00 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.60 50.0 4.47e-01 96.5% 69.4%
6j8eA01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.60 41.0 3.49e-01 73.7% 70.8%
2ys8A00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.56 43.0 3.86e-01 89.5% 76.7%
2raaA00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.53 44.0 3.24e-01 98.2% 88.8%
1te2A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 39.0 3.69e-01 82.5% 75.0%
2jx0A00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.52 43.0 3.44e-01 98.2% 67.9%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3730705 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.87 67.0 7.18e-01 82.5% 92.0%
3619900 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.83 65.0 6.23e-01 84.2% 87.7%
3522325 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.82 64.0 6.11e-01 84.2% 72.3%
3928087 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.80 64.0 5.96e-01 87.7% 70.0%
3365315 101.1.1.291 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PF26175 0.78 60.0 6.12e-01 82.5% 89.1%
3602903 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.77 54.0 5.16e-01 82.5% 64.6%
3434511 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.76 60.0 5.73e-01 84.2% 73.8%
2138992 182.1.3.1 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › PriX 0.74 64.0 5.25e-01 100.0% 64.5%
3234099 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.72 60.0 5.73e-01 91.2% 81.5%
3234027 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.70 53.0 5.28e-01 86.0% 80.0%
3238309 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.70 55.0 5.30e-01 87.7% 81.5%
4336911 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.69 57.0 5.39e-01 93.0% 87.1%
3176271 2007.2.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase2 0.69 60.0 4.16e-01 100.0% 72.3%
3266370 2007.2.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase2 0.68 58.0 4.20e-01 100.0% 82.3%
4110342 2007.2.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase2 0.67 58.0 4.14e-01 100.0% 88.6%
5016537 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.66 47.0 2.84e-01 77.2% 12.5%
3673343 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 0.59 47.0 3.99e-01 94.7% 86.7%
3439392 185.1.1.3 ↗ alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin › Hydrophob_seed 0.58 49.0 4.68e-01 100.0% 95.7%
4015399 4048.1.1.1 ↗ alpha bundles › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Catalase-rel 0.56 46.0 4.20e-01 100.0% 70.6%
1883370 3455.1.1.5 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors › PexRD54_WY 0.55 45.0 4.38e-01 100.0% 97.0%
D3 high residues 136-212
PDB
Domain cluster: rep: NC_051679.1__YP_009959344.1__I5H59_gp79__00079__D6-95
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z5bB03 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.62 45.0 3.71e-01 77.9% 67.8%
3cu3A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 50.0 3.99e-01 92.2% 76.5%
3bwnD01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 52.0 4.24e-01 100.0% 72.2%
2ia1A01 3.30.500.20 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › BH3703-like domains 0.58 42.0 3.71e-01 100.0% 50.4%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 46.0 4.69e-01 88.3% 97.3%
5wpjA02 3.30.70.420 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain 0.58 47.0 4.29e-01 92.2% 75.0%
1di2A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 46.0 4.79e-01 88.3% 98.6%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.57 50.0 3.38e-01 100.0% 30.3%
1vw4502 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 46.0 4.36e-01 89.6% 78.3%
4bhqA00 3.30.70.2830 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 41.0 3.73e-01 80.5% 96.3%
1egaA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.56 47.0 4.19e-01 90.9% 85.8%
2nugB02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 44.0 4.56e-01 88.3% 95.8%
2kcjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 32.0 2.96e-01 71.4% 39.8%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 41.0 3.44e-01 83.1% 99.3%
5gneA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 47.0 3.27e-01 100.0% 32.6%
4wy5A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 45.0 3.10e-01 100.0% 89.1%
3ko2A00 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.53 38.0 3.08e-01 76.6% 54.7%
6secA03 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 45.0 3.16e-01 100.0% 88.0%
3ue2A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 44.0 4.21e-01 93.5% 81.8%
4aw8A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 39.0 3.05e-01 93.5% 34.9%
5u3fB01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.51 39.0 3.25e-01 81.8% 56.4%
2mqdA00 3.30.1460.60 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.51 42.0 3.74e-01 96.1% 63.9%
4rx6D00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 38.0 3.49e-01 83.1% 69.2%
3s1tA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.50 39.0 3.89e-01 93.5% 82.5%
3n91A02 2.40.128.420 Mainly Beta › Beta Barrel › Lipocalin › 0.50 37.0 3.25e-01 83.1% 98.5%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010581 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.69 55.0 4.74e-01 84.4% 80.9%
4941612 212.1.1.22 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Topo-VIb_trans 0.66 48.0 3.46e-01 77.9% 47.0%
4443422 212.1.1.22 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Topo-VIb_trans 0.65 47.0 3.53e-01 77.9% 53.5%
3313182 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.64 48.0 5.05e-01 100.0% 87.1%
3718671 304.55.2.0 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.63 45.0 3.10e-01 94.8% 22.7%
3264034 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.62 48.0 5.18e-01 100.0% 95.4%
3934685 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 47.0 4.64e-01 88.3% 82.4%
4545039 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 48.0 5.01e-01 94.8% 100.0%
4957038 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.58 51.0 3.44e-01 100.0% 28.5%
4971376 2011.1.1.0 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases 0.57 51.0 3.44e-01 100.0% 29.3%
3170588 2011.1.1.0 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases 0.57 51.0 3.42e-01 100.0% 32.4%
3994634 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.57 50.0 3.32e-01 100.0% 27.1%
3602520 304.126.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.57 36.0 3.66e-01 72.7% 65.3%
5064863 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.56 49.0 4.33e-01 100.0% 93.0%
3993916 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.56 49.0 4.37e-01 98.7% 89.1%
3953070 243.1.1.80 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26580 0.56 48.0 4.27e-01 96.1% 98.2%
3670573 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.55 37.0 2.81e-01 76.6% 28.1%
4215835 327.11.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KH_2 0.55 46.0 4.22e-01 92.2% 89.3%
5055411 2011.1.1.6 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20 0.55 39.0 2.73e-01 74.0% 57.4%
3392320 304.166.1.9 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 0.55 44.0 3.89e-01 93.5% 58.3%
3624599 304.166.1.9 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 0.55 42.0 3.69e-01 98.7% 53.3%
135631 4090.1.1.1 ↗ a+b two layers › BH3703-like › BH3703-like › BH3703-like › YezG-like 0.54 40.0 3.20e-01 100.0% 37.0%
4878713 331.3.1.42 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Mtb12_C 0.54 41.0 3.79e-01 83.1% 98.0%
3246937 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.54 42.0 4.39e-01 85.7% 94.3%
4609849 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.53 36.0 3.47e-01 70.1% 83.3%
3728856 171.1.1.9 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3, Ribonucleas_3_3 0.53 45.0 3.28e-01 97.4% 75.1%
3619787 63.1.1.6 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › MRH_ELAPOR1_9th 0.52 43.0 3.40e-01 97.4% 74.5%
5048142 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.52 43.0 2.62e-01 100.0% 54.3%
3940290 63.1.1.6 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › MRH_ELAPOR1_9th 0.52 41.0 3.41e-01 97.4% 82.9%
1681454 304.166.1.9 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 0.51 41.0 3.64e-01 93.5% 58.6%
3772995 304.166.1.9 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 0.51 42.0 3.60e-01 94.8% 55.2%
3214339 63.1.1.6 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › MRH_ELAPOR1_9th 0.51 42.0 3.26e-01 100.0% 81.4%
3297153 11.1.1.808 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7036 0.51 40.0 3.54e-01 90.9% 89.6%
4018452 7579.1.1.36 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.51 42.0 2.96e-01 100.0% 94.4%
3310467 304.166.1.3 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › DUF7036 0.50 40.0 3.52e-01 90.9% 89.6%
3963977 304.162.1.0 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.50 38.0 3.77e-01 89.6% 76.5%
3274387 11.1.5.62 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › CBM49 0.50 36.0 3.30e-01 79.2% 94.5%