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MW314850.1__QPO17094.1__SEA_LILBEANIE_16__00016

Bact-Vir

MW314850.1__QPO17094.1__SEA_LILBEANIE_16__00016

Identity

Accession:
MW314850 ↗
Kingdom:
phage

Quality

73.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Lilbeanievirus› Gordonia_phage_Lilbeanie

TaxID: 2794947

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 17-171
PDB
Domain cluster: rep: OR521081.1__WNO27886.1__SEA_HALO3_17__00017__D18-170
D2 high residues 394-536
PDB
Domain cluster: rep: MT310852.1__QJD49729.1__SEA_CLUBPENGUIN_5__00005__D26-178
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13563.13 best 2_5_RNA_ligase2 34.8 2.30e-08 88.8% 67.8%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4h7wA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.85 81.0 7.29e-01 100.0% 96.8%
1iuhA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.84 79.0 7.17e-01 100.0% 96.2%
1jh6A00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.82 78.0 7.11e-01 100.0% 93.9%
2vfkA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.82 77.0 6.71e-01 100.0% 95.6%
1vdxA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.81 76.0 6.95e-01 100.0% 97.3%
2d4gA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.80 74.0 7.05e-01 100.0% 98.2%
4qakA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.79 73.0 6.89e-01 100.0% 96.5%
2fsqA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.74 68.0 5.76e-01 100.0% 84.5%
2b5iB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 28.0 3.31e-01 100.0% 69.1%
6mavB02 2.40.50.120 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 28.0 3.35e-01 92.3% 80.5%
ECOD (72)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3680289 264.1.1.0 ↗ beta barrels › LigT-like › LigT-related › LigT-related 0.89 85.0 7.54e-01 100.0% 99.0%
4951796 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.87 83.0 7.28e-01 100.0% 98.0%
3479830 264.1.1.0 ↗ beta barrels › LigT-like › LigT-related › LigT-related 0.86 82.0 7.28e-01 100.0% 94.4%
3821993 264.1.1.0 ↗ beta barrels › LigT-like › LigT-related › LigT-related 0.86 82.0 6.56e-01 100.0% 77.5%
3955687 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.86 80.0 7.59e-01 97.2% 98.8%
3962197 264.1.1.0 ↗ beta barrels › LigT-like › LigT-related › LigT-related 0.86 82.0 7.67e-01 100.0% 98.8%
2322578 264.1.1.6 ↗ beta barrels › LigT-like › LigT-related › LigT-related › HVSL 0.85 81.0 7.33e-01 100.0% 96.2%
5011802 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.85 81.0 7.01e-01 100.0% 84.4%
3397353 264.1.1.6 ↗ beta barrels › LigT-like › LigT-related › LigT-related › HVSL 0.85 80.0 7.30e-01 100.0% 96.7%
5019632 264.1.1.0 ↗ beta barrels › LigT-like › LigT-related › LigT-related 0.85 80.0 6.84e-01 100.0% 94.5%
5039548 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.84 80.0 7.32e-01 100.0% 97.2%
277 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.84 79.0 7.17e-01 100.0% 96.2%
5042461 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.83 78.0 7.07e-01 100.0% 96.8%
4453123 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.83 78.0 7.19e-01 100.0% 98.3%
3739681 264.1.1.6 ↗ beta barrels › LigT-like › LigT-related › LigT-related › HVSL 0.83 78.0 6.91e-01 100.0% 97.5%
3338135 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.83 79.0 7.18e-01 100.0% 94.4%
4982807 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.82 78.0 7.05e-01 100.0% 97.8%
None — 0.82 77.0 7.11e-01 100.0% 97.8%
None — 0.82 77.0 7.18e-01 100.0% 98.9%
4956981 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.82 77.0 7.02e-01 100.0% 96.8%
3270425 264.1.1.6 ↗ beta barrels › LigT-like › LigT-related › LigT-related › HVSL 0.82 78.0 6.89e-01 100.0% 97.9%
276 264.1.1.4 ↗ beta barrels › LigT-like › LigT-related › LigT-related › CPDase 0.82 78.0 7.11e-01 100.0% 93.9%
5029239 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.82 77.0 7.11e-01 100.0% 97.8%
4946449 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.82 77.0 7.00e-01 100.0% 97.3%
3253597 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.81 77.0 6.82e-01 100.0% 97.9%
5036038 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.81 76.0 6.98e-01 99.3% 98.3%
None — 0.81 76.0 6.95e-01 100.0% 97.3%
4972958 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.81 76.0 6.96e-01 100.0% 97.8%
5061864 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.81 75.0 6.85e-01 98.6% 94.6%
4952280 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.81 76.0 6.99e-01 100.0% 99.4%
4968059 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.81 76.0 6.98e-01 100.0% 97.8%
None — 0.81 75.0 6.87e-01 100.0% 97.3%
1117634 264.1.1.8 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS,AKAP7_RIRII_bdg 0.81 76.0 6.35e-01 100.0% 85.2%
5030633 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.81 75.0 6.82e-01 100.0% 95.7%
3616225 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.81 75.0 6.43e-01 100.0% 91.8%
4937535 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 76.0 7.03e-01 100.0% 98.9%
None — 0.80 72.0 6.73e-01 94.4% 99.4%
4930187 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 75.0 6.80e-01 100.0% 96.3%
4994515 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 6.91e-01 100.0% 98.3%
4046553 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 7.07e-01 100.0% 96.5%
4948034 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 75.0 6.84e-01 100.0% 96.2%
4949121 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 75.0 6.92e-01 100.0% 97.8%
None — 0.80 75.0 7.06e-01 100.0% 97.0%
5047137 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 75.0 6.82e-01 100.0% 96.8%
5067404 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 6.81e-01 100.0% 96.2%
4967857 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 73.0 6.69e-01 97.2% 97.8%
5051264 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 6.93e-01 100.0% 97.7%
4031839 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 7.04e-01 100.0% 97.6%
5010662 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.80 75.0 6.78e-01 100.0% 96.2%
3982264 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.80 74.0 6.91e-01 100.0% 96.0%
3531648 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.79 74.0 6.83e-01 100.0% 98.9%
3738455 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.79 74.0 6.62e-01 100.0% 99.0%
1953031 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.79 74.0 6.86e-01 100.0% 95.4%
4972305 264.1.1.7 ↗ beta barrels › LigT-like › LigT-related › LigT-related › AKAP7_NLS 0.79 74.0 6.85e-01 100.0% 97.8%
4942504 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.79 73.0 6.72e-01 100.0% 97.8%
4423124 264.1.1.15 ↗ beta barrels › LigT-like › LigT-related › LigT-related › DUF1045 0.79 74.0 6.20e-01 100.0% 98.7%
4957217 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.79 74.0 6.76e-01 100.0% 97.2%
4965540 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.79 73.0 6.67e-01 100.0% 98.4%
5055911 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.79 73.0 6.77e-01 100.0% 97.8%
5028063 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.78 74.0 6.84e-01 100.0% 96.6%
5063905 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.78 73.0 6.87e-01 100.0% 97.6%
4965442 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.78 72.0 6.94e-01 99.3% 100.0%
4979619 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.78 69.0 6.48e-01 94.4% 98.8%
5058094 264.1.1.1 ↗ beta barrels › LigT-like › LigT-related › LigT-related › LigT_PEase 0.77 72.0 6.71e-01 100.0% 98.9%
5062926 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.77 72.0 6.87e-01 100.0% 96.4%
4991838 264.1.1.9 ↗ beta barrels › LigT-like › LigT-related › LigT-related › 2_5_RNA_ligase2 0.76 64.0 6.70e-01 88.1% 98.5%
3744887 264.1.1.10 ↗ beta barrels › LigT-like › LigT-related › LigT-related › tRNA_lig_CPD 0.58 51.0 4.82e-01 93.0% 99.4%
5042268 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.56 42.0 4.63e-01 95.1% 99.1%
5005180 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.55 44.0 4.70e-01 95.8% 99.2%
3969377 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 27.0 3.57e-01 93.7% 91.9%
3472865 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.53 42.0 4.47e-01 95.8% 97.6%
4929367 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.51 40.0 4.29e-01 95.1% 98.3%
D3 medium residues 210-285
PDB
D4 medium residues 286-351
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6fakA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.67 46.0 4.33e-01 72.7% 59.3%
3mvpA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.66 56.0 4.36e-01 95.5% 59.1%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.66 54.0 5.18e-01 92.4% 94.9%
1q1vA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.65 51.0 5.10e-01 97.0% 84.3%
8e9gE01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.64 47.0 4.78e-01 93.9% 84.1%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.63 53.0 4.97e-01 98.5% 75.6%
3dewA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.63 52.0 4.13e-01 93.9% 64.3%
1qd1B02 3.30.70.670 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Formiminotransferase, C-terminal subdomain 0.61 46.0 3.66e-01 84.8% 55.9%
5hexA01 3.40.367.20 Alpha Beta › 3-Layer(aba) Sandwich › Hexokinase; domain 1 › 0.60 51.0 3.44e-01 98.5% 24.5%
1twfB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.60 45.0 3.39e-01 81.8% 65.5%
2vvwA00 1.10.437.20 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus 0.57 49.0 3.85e-01 100.0% 68.0%
1d3yA01 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 0.57 45.0 4.49e-01 93.9% 88.7%
1b8bA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.57 44.0 2.65e-01 86.4% 21.6%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.55 36.0 3.66e-01 72.7% 68.2%
1f5mA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.53 42.0 3.27e-01 93.9% 88.6%
4g6uA01 6.10.140.1810 Special › Helix non-globular › Helix Hairpins › 0.53 36.0 3.69e-01 92.4% 75.8%
4h0oA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 41.0 2.97e-01 92.4% 91.2%
1vb3A01 3.90.1380.10 Alpha Beta › Alpha-Beta Complex › threonine synthase, domain 1, chain A › Threonine synthase, N-terminal domain 0.51 40.0 3.77e-01 86.4% 81.5%
1ekjA00 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.50 37.0 2.66e-01 90.9% 25.2%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3886806 108.1.1.28 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 0.76 54.0 4.82e-01 74.2% 62.2%
4532731 101.1.17.1 ↗ alpha arrays › HTH › HTH › FF domain › Ribosomal_S17e 0.75 59.0 5.69e-01 95.5% 74.7%
3420171 108.1.1.1 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1 0.70 50.0 4.80e-01 74.2% 70.7%
3590988 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.69 56.0 4.41e-01 87.9% 44.4%
3441094 101.1.2.252 ↗ alpha arrays › HTH › HTH › winged helix domain › OHA 0.69 60.0 5.70e-01 100.0% 88.7%
3656425 108.1.1.29 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 0.69 48.0 4.48e-01 72.7% 65.0%
171404 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.66 54.0 5.18e-01 92.4% 94.9%
3467989 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.65 53.0 5.51e-01 95.5% 96.7%
3683998 108.1.1.97 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_7 0.65 53.0 4.43e-01 87.9% 75.5%
4520559 592.2.1.1 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like › DUF1871 0.65 53.0 4.99e-01 95.5% 75.3%
3229051 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 51.0 4.96e-01 90.9% 86.7%
4235797 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.62 51.0 3.84e-01 93.9% 38.9%
4456963 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.60 48.0 3.64e-01 95.5% 38.4%
4961900 101.1.1.187 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_33 0.59 49.0 4.79e-01 98.5% 85.3%
5063554 101.1.2.894 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF2240 0.59 46.0 3.74e-01 89.4% 77.8%
4968187 101.1.2.619 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_33 0.57 49.0 5.00e-01 98.5% 100.0%
3691294 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.55 43.0 4.01e-01 87.9% 96.5%
3652921 309.1.1.4 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C 0.53 44.0 3.10e-01 98.5% 74.9%
1681684 244.1.1.9 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › GMC_oxred_C 0.52 40.0 2.95e-01 87.9% 41.4%