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js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00208

Bact-Vir

js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00208

Identity

Kingdom:
phage

Quality

72.6 mean pLDDT

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 4-58
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14207.12 best DpnD-PcfM 27.4 3.40e-06 81.8% 95.7%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2m38A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 37.0 2.92e-01 74.5% 43.0%
3htxA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 35.0 3.31e-01 96.4% 50.0%
3vtiA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 38.0 3.17e-01 76.4% 83.3%
3hx9B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 39.0 3.30e-01 83.6% 99.0%
3gr3A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.52 40.0 2.78e-01 89.1% 58.0%
3dzaA02 6.10.250.2140 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 37.0 3.63e-01 78.2% 83.9%
1tr0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 3.22e-01 87.3% 100.0%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4293895 3115.2.1.2 ↗ a+b two layers › GP2-like › GP2 › GP2 › DpnD-PcfM 0.96 67.0 7.88e-01 72.7% 100.0%
3519907 3333.1.1.1 ↗ a+b two layers › Barrel domain in dedicator of cytokinesis protein 9 › Barrel domain in dedicator of cytokinesis protein 9 › Barrel domain in dedicator of cytokinesis protein 9 › DHR-2_Lobe_B 0.66 40.0 2.85e-01 100.0% 20.0%
3719511 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.59 41.0 2.50e-01 72.7% 39.7%
3708379 5.1.5.208 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › EMC1_C, PQQ_2, Beta-prop_EMC1_N 0.55 46.0 2.58e-01 100.0% 9.0%
3614893 2004.1.1.493 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA, AAA_2, AAA_5 0.54 44.0 2.82e-01 100.0% 49.1%
4166586 2004.1.1.429 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_15 0.54 38.0 2.34e-01 74.5% 43.6%
3201653 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.53 44.0 2.72e-01 100.0% 48.4%
3415261 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.51 35.0 2.65e-01 72.7% 39.4%
334601 244.1.1.4 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › DAO 0.50 42.0 3.48e-01 96.4% 97.1%
3231115 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.50 40.0 2.74e-01 96.4% 86.9%
D2 high residues 87-154
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5jajA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.66 57.0 4.81e-01 97.1% 93.1%
1ad6A00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.65 56.0 4.17e-01 100.0% 59.5%
2ah5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.62 44.0 4.49e-01 100.0% 78.5%
7ebcA01 1.10.10.850 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.61 51.0 4.36e-01 97.1% 87.1%
3ikhA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.61 46.0 3.10e-01 85.3% 86.4%
3b0cW00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.58 41.0 4.05e-01 75.0% 94.5%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.56 41.0 4.18e-01 85.3% 83.3%
5je8B02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.55 38.0 3.14e-01 72.1% 46.9%
6n2nA01 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.55 46.0 3.55e-01 100.0% 91.6%
3zfvA02 3.30.70.1900 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 3.55e-01 100.0% 65.4%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5061617 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.66 56.0 3.39e-01 94.1% 26.4%
4015024 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.60 48.0 2.97e-01 91.2% 25.9%
4411945 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.57 47.0 4.21e-01 94.1% 82.0%
4968341 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 48.0 3.22e-01 98.5% 35.1%
3413469 7579.1.1.89 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › COesterase, BD-FAE 0.54 45.0 2.72e-01 94.1% 59.4%
3761824 101.1.1.21 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_Tc5 0.52 38.0 3.81e-01 82.4% 84.3%