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NC_054890.1__YP_010064510.1__KMB82_gp43__00043

Bact-Vir

NC_054890.1__YP_010064510.1__KMB82_gp43__00043

Identity

Accession:
NC_054890 ↗
Kingdom:
phage

Quality

95.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Autotranscriptaviridae› Warsawvirus› Pseudomonas_phage_vB_PsyP_3MF5

TaxID: 2749426

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 medium residues 5-68
PDB
Domain cluster: rep: JN991020.1__AEX65881.1__BF7_00215__00042__D5-63
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bm4A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.64 43.0 3.01e-01 76.6% 22.3%
1ae2A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 47.0 4.26e-01 82.8% 97.7%
2cc3A00 3.10.450.230 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › VirB8 protein 0.61 48.0 3.73e-01 87.5% 79.2%
5h9kA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 47.0 3.60e-01 85.9% 44.8%
5c7qB00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.60 45.0 3.32e-01 82.8% 64.4%
4f98A00 2.30.140.50 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Protein of unknown function DUF2790 0.60 39.0 3.97e-01 90.6% 69.4%
5tgnA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 47.0 3.96e-01 87.5% 82.6%
1g19A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 45.0 3.20e-01 87.5% 83.5%
3uc2A00 2.60.40.3340 Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4426 0.58 42.0 3.46e-01 78.1% 68.5%
3nqzA01 3.10.450.490 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 43.0 3.86e-01 81.2% 60.4%
4kcaA02 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.57 48.0 2.98e-01 96.9% 16.0%
4amwA01 2.60.40.1760 Mainly Beta › Sandwich › Immunoglobulin-like › glycosyl hydrolase (family 31) 0.57 50.0 3.17e-01 96.9% 32.4%
2vckA00 3.40.1500.20 Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase › 0.57 38.0 2.76e-01 70.3% 23.6%
1u17A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 43.0 3.15e-01 84.4% 45.4%
2jq5A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 43.0 3.55e-01 87.5% 68.8%
5kkuD00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.56 40.0 2.68e-01 78.1% 34.9%
2f86B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 44.0 3.55e-01 87.5% 82.2%
2hhiA01 3.30.565.40 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Fervidobacterium nodosum Rt17-B1 like 0.55 40.0 3.41e-01 81.2% 75.4%
4hgzA02 2.20.25.570 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.55 34.0 3.55e-01 73.4% 66.7%
1gr0A02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.55 38.0 3.55e-01 73.4% 82.1%
4fpvB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 37.0 2.57e-01 73.4% 23.0%
4hrzB00 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 38.0 3.22e-01 78.1% 42.3%
1yqzA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.54 45.0 3.92e-01 100.0% 77.8%
1l3wA02 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.53 38.0 3.17e-01 75.0% 75.0%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.53 42.0 3.51e-01 90.6% 69.1%
5dmyA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 42.0 3.55e-01 92.2% 97.5%
2fujA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.53 39.0 3.23e-01 79.7% 89.0%
4fx9A03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.53 45.0 3.84e-01 100.0% 72.6%
1nhpA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.53 44.0 3.81e-01 100.0% 73.5%
3kg7B00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.53 40.0 2.70e-01 85.9% 85.3%
3g0kA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 38.0 3.15e-01 81.2% 69.5%
5tseA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.52 39.0 3.24e-01 87.5% 83.1%
3cjeA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 39.0 3.09e-01 89.1% 36.7%
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.52 36.0 3.62e-01 76.6% 74.6%
7usrA01 2.60.40.2860 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 35.0 2.86e-01 73.4% 97.8%
4kwyA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.51 40.0 3.26e-01 89.1% 70.8%
5w8mA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.51 37.0 2.66e-01 76.6% 36.2%
2iqiB00 3.40.50.10610 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ABC-type transport auxiliary lipoprotein component 0.51 39.0 3.04e-01 89.1% 77.2%
3w1eA02 3.40.50.10610 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ABC-type transport auxiliary lipoprotein component 0.51 39.0 2.99e-01 89.1% 68.9%
4z9cB00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 41.0 3.53e-01 95.3% 56.5%
4cu7A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 40.0 3.38e-01 92.2% 97.5%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5037223 2.1.1.12 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S28e 0.71 48.0 4.95e-01 93.8% 75.0%
3953609 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.67 51.0 4.17e-01 81.2% 74.8%
3224838 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.66 49.0 3.13e-01 81.2% 38.5%
None — 0.65 51.0 3.25e-01 84.4% 40.7%
3668385 243.1.1.89 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF7074 0.65 51.0 4.62e-01 87.5% 78.9%
3563416 5095.1.1.0 ↗ beta sandwiches › N-terminal beta-sandwich domain in anthrax protective antigen › N-terminal beta-sandwich domain in anthrax protective antigen › N-terminal beta-sandwich domain in anthrax protective antigen 0.63 46.0 4.64e-01 78.1% 84.6%
3952896 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.63 52.0 4.16e-01 89.1% 75.0%
3278140 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.63 50.0 4.22e-01 87.5% 86.4%
3650282 243.5.1.8 ↗ a+b two layers › Cystatin-like › Amine oxidase N-terminal region › Amine oxidase N-terminal region › DUF7074 0.63 49.0 4.48e-01 87.5% 73.0%
3950922 243.1.1.80 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26580 0.62 52.0 4.21e-01 92.2% 81.7%
3450141 283.2.1.8 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › PF29994 0.61 44.0 3.90e-01 78.1% 57.0%
3658474 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.61 48.0 4.26e-01 87.5% 75.8%
3991433 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.60 44.0 3.41e-01 82.8% 61.6%
3230068 243.1.1.85 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26531 0.59 48.0 4.10e-01 92.2% 80.9%
3483288 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.59 43.0 3.48e-01 78.1% 42.3%
5000502 2.1.1.12 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S28e 0.59 51.0 4.68e-01 98.4% 77.6%
3728893 206.1.1.55 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › EcKL 0.58 42.0 2.71e-01 82.8% 28.1%
3286836 243.1.1.80 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26580 0.57 46.0 3.83e-01 89.1% 76.5%
3297629 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.57 41.0 3.84e-01 76.6% 63.7%
4534466 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.56 45.0 4.06e-01 93.8% 78.9%
4963204 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.56 45.0 3.27e-01 89.1% 63.2%
4237498 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.56 46.0 3.72e-01 92.2% 48.0%
3439646 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.55 46.0 4.05e-01 100.0% 72.4%
3407245 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.54 43.0 3.56e-01 90.6% 71.2%
4681738 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.54 46.0 3.48e-01 98.4% 43.0%
3225640 220.1.1.168 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Tmpp129 0.54 42.0 3.46e-01 87.5% 62.4%
3930170 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 37.0 3.21e-01 75.0% 84.5%
4940463 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.53 39.0 3.18e-01 81.2% 40.7%
3269706 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 43.0 4.10e-01 96.9% 96.2%
3631773 222.1.1.4 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT 0.53 42.0 3.12e-01 89.1% 70.3%
4003463 220.1.1.168 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Tmpp129 0.53 42.0 3.50e-01 92.2% 64.8%
4355192 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.53 38.0 3.00e-01 81.2% 68.8%
3621723 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.53 44.0 3.06e-01 98.4% 32.4%
4241432 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.53 44.0 3.66e-01 100.0% 52.8%
4679671 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.52 44.0 3.71e-01 98.4% 89.8%
3177409 330.1.1.13 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Mgm101p 0.52 42.0 3.17e-01 90.6% 40.0%
3254982 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.52 37.0 3.70e-01 81.2% 85.7%
2387841 11.1.1.142 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DsbD_N 0.50 43.0 3.38e-01 100.0% 81.8%
5055184 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.50 38.0 3.54e-01 85.9% 69.4%
4642685 7503.1.1.3 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › TolB_N 0.50 39.0 3.20e-01 87.5% 65.6%
D2 medium residues 81-119
PDB
Domain cluster: rep: NC_042054.1__YP_009616759.1__FDI83_gp131__00073__D101-138