←Back to structures

ON464759.1__UTV60802.1__JDFnp1_14__00014

Bact-Vir

ON464759.1__UTV60802.1__JDFnp1_14__00014

Identity

Accession:
ON464759 ↗
Kingdom:
phage

Quality

85.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Fusobacterium_phage_JD-Fnp1

TaxID: 2950463

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 510-656
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5tw1D01 1.10.274.100 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › RNA polymerase Rpb1, domain 3 0.68 64.0 6.49e-01 98.6% 100.0%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.61 33.0 4.31e-01 83.7% 97.4%
1twfA05 1.10.274.100 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › RNA polymerase Rpb1, domain 3 0.54 48.0 4.72e-01 100.0% 88.9%
3rc3A01 1.10.1740.140 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.52 27.0 3.09e-01 100.0% 67.0%
1vx7X00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.51 26.0 3.12e-01 98.6% 71.1%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4516064 4959.1.1.1 ↗ a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 0.70 65.0 6.51e-01 100.0% 96.0%
4059731 101.1.1.64 ↗ alpha arrays › HTH › HTH › Three-helical HTH › tRNA_bind_2 0.58 31.0 3.50e-01 100.0% 66.7%
3167174 109.46.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) 0.54 37.0 3.32e-01 83.0% 50.0%
3179847 109.4.1.681 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans_2 0.52 39.0 2.88e-01 78.2% 61.8%
D2 high residues 669-765
PDB
Domain cluster: rep: MG592415.1__AUR83112.1__NVP1031O_130__00130__D624-731
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.84 75.0 6.54e-01 94.8% 79.7%
4kn7D01 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.79 69.0 6.21e-01 95.9% 94.7%
7s00D01 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.77 69.0 6.39e-01 100.0% 77.9%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.57 40.0 4.44e-01 82.5% 93.5%
2js9A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.56 40.0 4.27e-01 94.8% 87.7%
3u8vA00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.56 41.0 4.39e-01 92.8% 91.6%
2wmoA01 1.25.40.410 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › DOCK DHR2 domain, lobe A 0.55 42.0 3.79e-01 80.4% 64.9%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.54 38.0 4.25e-01 82.5% 96.0%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.53 36.0 3.54e-01 74.2% 64.1%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 37.0 4.07e-01 81.4% 94.6%
2i0mA02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.52 40.0 3.98e-01 83.5% 92.1%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.52 41.0 3.86e-01 93.8% 69.4%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 39.0 3.43e-01 82.5% 88.2%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.51 39.0 3.91e-01 82.5% 87.3%
1vctA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.51 40.0 3.87e-01 83.5% 80.7%
3fhnA03 1.10.357.100 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Dsl1p vesicle tethering complex, Tip20p subunit, domain C 0.50 41.0 3.40e-01 88.7% 60.9%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.50 38.0 3.89e-01 82.5% 94.9%
6vynC01 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.50 33.0 3.59e-01 91.8% 85.1%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3959563 4958.1.1.0 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit 0.81 75.0 5.55e-01 100.0% 48.5%
4887358 4958.1.1.4 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 0.79 73.0 6.06e-01 100.0% 72.7%
4647018 4958.1.1.2 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 0.79 72.0 5.79e-01 100.0% 62.8%
4325839 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.57 40.0 4.54e-01 81.4% 100.0%
3918871 109.4.1.3569 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_12, Consortin_N 0.57 38.0 3.02e-01 82.5% 33.0%
4927880 601.16.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase 0.54 44.0 4.20e-01 92.8% 75.7%
3252144 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.54 37.0 4.23e-01 82.5% 100.0%
3710139 604.13.1.0 ↗ alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like 0.54 37.0 3.42e-01 82.5% 54.4%
5036828 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.53 46.0 3.84e-01 100.0% 81.7%
3592496 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 40.0 3.13e-01 80.4% 53.2%
4099122 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.51 45.0 3.44e-01 99.0% 80.9%
D3 medium residues 1-63_150-238
PDB
Domain cluster: rep: putative_RNA_polymerase_largest_subunit__YP_009001703__Anomala_cuprea_entomopoxvirus__62099__D13-74_212-273
D4 medium residues 64-149
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4id8A00 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 31.0 3.42e-01 98.8% 70.8%
3flkA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.52 46.0 3.09e-01 100.0% 90.5%
1q45A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 41.0 2.77e-01 89.5% 39.7%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3743565 109.4.1.313 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UTP20_N 0.57 40.0 2.74e-01 72.1% 40.0%
D5 medium residues 239-271_380-399_455-504
PDB
Domain cluster: rep: DNA-dependent_RNA_polymerase_subunit_rpo147__YP_232980__Vaccinia_virus__10245__D277-311_370-443
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ynjD04 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.83 70.0 6.13e-01 87.4% 100.0%
1twfA03 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.82 70.0 7.14e-01 88.3% 100.0%
7eu1A01 1.10.274.100 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › RNA polymerase Rpb1, domain 3 0.81 76.0 6.73e-01 100.0% 97.2%
1zc1A01 2.40.40.50 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › Ubiquitin fusion degradation protein UFD1, N-terminal domain 0.69 52.0 5.27e-01 78.6% 98.1%
1auvA01 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.60 35.0 4.46e-01 70.9% 100.0%
1gsaA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.60 37.0 4.60e-01 71.8% 100.0%
3tqtA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.57 37.0 4.43e-01 73.8% 100.0%
5d8dD03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.56 35.0 4.18e-01 71.8% 100.0%
2i87A03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.53 36.0 4.11e-01 72.8% 100.0%
5zctA02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.53 33.0 3.93e-01 70.9% 100.0%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081033 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.84 81.0 6.24e-01 100.0% 92.0%
5058903 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.84 79.0 6.19e-01 98.1% 95.8%
3509068 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.83 75.0 5.84e-01 94.2% 92.0%
4026183 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.83 77.0 6.65e-01 97.1% 100.0%
3684523 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.83 79.0 7.34e-01 100.0% 94.4%
4886549 275.1.1.1 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_2 0.83 79.0 6.74e-01 100.0% 99.4%
3966248 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.83 79.0 7.61e-01 100.0% 98.3%
4948679 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.83 76.0 5.09e-01 95.1% 53.4%
3836120 275.1.1.1 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_2 0.83 78.0 6.07e-01 98.1% 100.0%
4015760 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.82 77.0 6.04e-01 98.1% 97.4%
3670775 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 79.0 7.40e-01 100.0% 98.3%
4129914 1.1.2.31 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2, RNA_pol_Rpb1_3 0.82 78.0 5.94e-01 100.0% 72.1%
3596090 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.82 78.0 7.31e-01 99.0% 99.2%
4943460 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 78.0 6.24e-01 100.0% 96.8%
3360997 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 78.0 6.83e-01 100.0% 93.8%
3374701 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 78.0 6.29e-01 100.0% 95.6%
1746098 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 78.0 6.43e-01 100.0% 93.5%
3698542 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.82 78.0 6.01e-01 100.0% 95.1%
2886100 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.81 77.0 6.08e-01 100.0% 85.1%
4890084 1.1.2.31 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2, RNA_pol_Rpb1_3 0.79 73.0 6.85e-01 98.1% 93.4%
4887355 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.78 70.0 6.49e-01 93.2% 83.1%
2968637 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.76 68.0 5.66e-01 95.1% 98.2%
5042283 208.1.1.56 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › MazE_antitoxin 0.73 54.0 3.74e-01 76.7% 34.4%
3646137 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.69 60.0 4.74e-01 92.2% 98.5%
4967302 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.67 51.0 5.48e-01 79.6% 100.0%
4961166 1.1.2.23 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › PolC_DP2_cat 0.66 61.0 4.55e-01 100.0% 79.2%
5030460 1.1.2.23 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › PolC_DP2_cat 0.66 61.0 3.87e-01 100.0% 37.8%
3574276 11.1.4.112 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › DUF3694 0.51 36.0 3.24e-01 71.8% 80.0%
4383558 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 0.51 41.0 3.22e-01 89.3% 45.7%
D6 medium residues 272-379_400-454
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2k5cA00 3.10.20.830 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Bifunctional heparan sulphate n-deacetylase/n-sulphotransferase 0.65 26.0 3.47e-01 87.1% 67.0%
4lp8A01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 27.0 3.34e-01 95.7% 74.0%
1tuaA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.53 26.0 3.40e-01 75.5% 85.7%
2wcyA02 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.51 23.0 3.11e-01 73.0% 81.2%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3962658 106.1.1.6 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › MPAB_Lcp_cat 0.60 44.0 3.84e-01 76.7% 63.2%
3970718 3675.1.1.0 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain 0.54 29.0 3.02e-01 77.3% 54.0%
4429847 3675.1.1.1 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.53 29.0 2.90e-01 77.3% 49.1%
3964724 3675.1.1.1 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.50 25.0 2.61e-01 74.2% 46.5%
D7 medium residues 780-908
PDB
Domain cluster: representative
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4306501 275.1.1.4 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_5 0.77 69.0 5.96e-01 96.1% 80.4%
3207364 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.67 26.0 2.61e-01 100.0% 32.3%
4978692 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.51 31.0 2.34e-01 100.0% 24.9%