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MK533143.1__QBX06404.1__API480_71__00071

Bact-Vir

MK533143.1__QBX06404.1__API480_71__00071

Identity

Accession:
MK533143 ↗
Kingdom:
phage

Quality

95.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Paenibacillus_phage_vB_PlaP_API480

TaxID: 2530020

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 high residues 2-58
PDB
Domain cluster: rep: NC_048776.1__YP_009847575.1__HWC32_gp094__00094__D6-63
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l55A00 2.40.50.320 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Copper binding periplasmic protein CusF 0.74 58.0 5.11e-01 84.2% 95.1%
2f9wA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 47.0 3.63e-01 100.0% 31.3%
3pl5A03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.68 58.0 4.46e-01 100.0% 43.8%
3qf7A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 49.0 3.11e-01 100.0% 15.3%
4pz7A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.66 53.0 4.02e-01 89.5% 65.0%
6cngA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.66 59.0 4.51e-01 100.0% 47.7%
1x6oA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.65 49.0 4.46e-01 84.2% 98.7%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 42.0 3.50e-01 100.0% 36.9%
3fdjA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.63 56.0 4.33e-01 100.0% 47.7%
4wiqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 48.0 3.88e-01 80.7% 58.5%
1gsoA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.63 51.0 3.83e-01 87.7% 74.1%
3wnzA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.63 51.0 3.80e-01 89.5% 63.2%
2b5lB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.62 55.0 3.30e-01 100.0% 29.6%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 45.0 3.83e-01 100.0% 47.4%
3jr7A03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.61 54.0 4.20e-01 100.0% 48.0%
8f5pE01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.60 41.0 2.48e-01 100.0% 10.6%
3fdwA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.60 50.0 3.85e-01 93.0% 66.9%
3a58A01 2.30.29.90 Mainly Beta › Roll › PH-domain like › 0.60 52.0 3.66e-01 96.5% 36.2%
1e4eB01 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.59 48.0 3.49e-01 89.5% 67.3%
4qxaB00 2.30.29.230 Mainly Beta › Roll › PH-domain like › 0.59 40.0 3.10e-01 100.0% 28.6%
4iu2B01 2.60.40.3810 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 45.0 3.52e-01 82.5% 52.1%
3sreA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.58 51.0 3.15e-01 100.0% 21.6%
2h3gX02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 42.0 3.14e-01 80.7% 59.7%
1e3hA01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.58 42.0 2.80e-01 78.9% 19.8%
1ujcA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.57 45.0 3.26e-01 86.0% 99.4%
2h41A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 42.0 3.59e-01 80.7% 62.1%
2i87B02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 46.0 3.32e-01 89.5% 56.0%
2z04B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 50.0 3.47e-01 98.2% 82.8%
5h80B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 45.0 2.95e-01 87.7% 35.5%
3msyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 43.0 3.53e-01 100.0% 44.1%
6j9eJ00 3.30.160.560 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 42.0 4.06e-01 100.0% 72.7%
2fl4A02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 34.0 2.80e-01 80.7% 33.7%
6pxcA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.55 45.0 3.80e-01 100.0% 51.9%
1ehiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 44.0 3.31e-01 89.5% 72.9%
5dmxB02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 44.0 3.25e-01 89.5% 50.6%
3k5iA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 47.0 3.23e-01 96.5% 82.8%
3vpbB03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 44.0 3.54e-01 89.5% 75.9%
1ri6A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 48.0 2.98e-01 100.0% 19.8%
3lh4A00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 40.0 3.25e-01 80.7% 48.7%
1iowA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 44.0 3.25e-01 89.5% 64.4%
3buxB03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.54 39.0 3.50e-01 100.0% 53.5%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.54 43.0 4.12e-01 100.0% 72.7%
5oomJ01 3.30.1550.10 Alpha Beta › 2-Layer Sandwich › Ribosomal protein L11, N-terminal domain › Ribosomal protein L11/L12, N-terminal domain 0.54 37.0 3.64e-01 75.4% 100.0%
3hfqA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 47.0 2.91e-01 100.0% 20.0%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 43.0 3.21e-01 89.5% 72.2%
4f3nA00 3.40.50.12710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 39.0 2.43e-01 82.5% 50.8%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.53 46.0 3.60e-01 100.0% 48.1%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 45.0 3.12e-01 98.2% 83.7%
4o5fA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 44.0 3.50e-01 100.0% 71.7%
3qz4A00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 44.0 2.80e-01 100.0% 28.8%
3ci0J02 2.10.70.20 Mainly Beta › Ribbon › Complement Module; domain 1 › gspk-gspi-gspj complex like domains 0.51 36.0 3.83e-01 80.7% 88.0%
7c5wA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 36.0 2.72e-01 80.7% 29.1%
3d8pB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 42.0 3.18e-01 98.2% 63.7%
2je6A01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.50 36.0 2.43e-01 80.7% 18.0%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3439434 3521.1.1.3 ↗ a+b three layers › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › BRX 0.75 42.0 4.28e-01 80.7% 56.4%
3346566 1.1.7.85 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › BRX 0.74 41.0 4.19e-01 80.7% 56.4%
3376285 706.1.1.4 ↗ beta complex topology › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE › BRX 0.73 41.0 4.24e-01 80.7% 58.5%
3966083 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.71 49.0 3.90e-01 100.0% 35.7%
3306435 245.3.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Colicin S4 receptor-binding domain › Colicin S4 receptor-binding domain › BRX 0.71 38.0 3.96e-01 77.2% 53.7%
2507396 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.66 59.0 4.54e-01 100.0% 48.4%
4945379 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.64 58.0 4.44e-01 100.0% 48.8%
5054861 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.64 47.0 2.78e-01 100.0% 9.7%
4945438 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.64 57.0 4.35e-01 100.0% 46.9%
3671924 4325.1.1.12 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › AP2 0.63 42.0 4.64e-01 93.0% 100.0%
1937091 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.63 56.0 4.35e-01 100.0% 48.4%
4956002 2484.4.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like 0.63 52.0 4.29e-01 96.5% 58.2%
4329368 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.62 55.0 4.28e-01 100.0% 48.8%
4461189 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.62 55.0 4.24e-01 100.0% 48.8%
4158188 206.1.3.19 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.60 49.0 3.24e-01 89.5% 47.0%
4401930 2.1.1.31 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_ligase_A_C 0.60 44.0 3.52e-01 82.5% 85.3%
None — 0.59 49.0 3.25e-01 89.5% 45.1%
3415678 708.1.1.4 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FLYWCH 0.59 37.0 3.48e-01 78.9% 52.9%
4312097 295.1.1.15 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › UPF0128 0.58 48.0 3.35e-01 89.5% 73.7%
5052821 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 44.0 3.58e-01 80.7% 61.9%
3219070 5.1.3.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › WD40 0.57 49.0 2.79e-01 94.7% 11.5%
3609111 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 48.0 3.56e-01 96.5% 47.3%
4563304 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.56 50.0 3.09e-01 100.0% 19.8%
3215377 5.1.4.62 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PROPPIN 0.56 43.0 2.69e-01 100.0% 13.7%
4371091 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.56 50.0 3.06e-01 100.0% 22.2%
4203120 5.1.4.36 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › MMS1_N 0.55 48.0 2.83e-01 98.2% 31.9%
None — 0.55 48.0 2.91e-01 100.0% 16.4%
5056596 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.55 41.0 2.63e-01 86.0% 35.2%
3626322 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 47.0 2.82e-01 94.7% 18.6%
3382274 5.1.4.369 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › EMC1_C, Beta-prop_EMC1_N 0.54 48.0 2.66e-01 100.0% 7.6%
3534889 5.1.5.95 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Det1 0.54 48.0 2.82e-01 98.2% 18.3%
3379506 243.3.1.62 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PF26138 0.54 40.0 3.34e-01 80.7% 47.5%
3439990 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.54 39.0 3.42e-01 100.0% 50.0%
2429383 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.54 48.0 2.94e-01 100.0% 19.5%
3266245 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 47.0 3.64e-01 96.5% 51.7%
3566463 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.54 47.0 3.27e-01 96.5% 44.0%
3404944 5.1.4.235 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_IFT140_1st 0.54 48.0 2.82e-01 100.0% 25.1%
3785954 5.1.3.154 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PF30361 0.53 46.0 2.80e-01 100.0% 16.5%
3309808 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.53 48.0 3.17e-01 100.0% 30.9%
3480913 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.53 38.0 3.47e-01 80.7% 55.3%
3678427 5.1.4.379 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, WD40_2 0.53 44.0 2.80e-01 100.0% 17.5%
4025071 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.53 38.0 3.43e-01 80.7% 53.4%
4527067 206.1.3.40 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.53 42.0 2.78e-01 89.5% 42.4%
4660425 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.52 41.0 3.42e-01 100.0% 46.1%
4037298 76.1.1.1 ↗ beta duplicates or obligate multimers › beta-Prism I › beta-Prism I › beta-Prism I › Endotoxin_M 0.52 36.0 2.58e-01 73.7% 48.0%
3640086 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 45.0 2.79e-01 100.0% 24.8%
3932499 5.1.11.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed 0.52 46.0 2.80e-01 100.0% 22.6%
4941120 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 44.0 3.21e-01 98.2% 51.2%
2388639 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.52 37.0 3.24e-01 80.7% 47.5%
4965528 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 36.0 2.45e-01 96.5% 18.7%
3294274 5.1.5.95 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Det1 0.52 46.0 2.68e-01 100.0% 25.7%
3827487 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 42.0 2.56e-01 100.0% 14.9%
4435421 5.1.4.271 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, PF30361 0.51 43.0 2.61e-01 100.0% 28.8%
3893892 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.51 39.0 3.62e-01 89.5% 100.0%
1156978 3735.1.1.2 ↗ beta meanders › Rearrangement hotspot (RHS) repeats protein › Rearrangement hotspot (RHS) repeats protein › Rearrangement hotspot (RHS) repeats protein › SpvB,TcdB_toxin_midC,TcdB_toxin_midN 0.50 44.0 2.66e-01 100.0% 25.9%
5033562 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.50 36.0 3.32e-01 80.7% 58.7%