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KX905163.1__ARB07115.1__Semix9P1_phi72__00072

Bact-Vir

KX905163.1__ARB07115.1__Semix9P1_phi72__00072

Identity

Accession:
KX905163 ↗
Kingdom:
phage

Quality

90.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Clostridioides_phage_phiSemix9P1

TaxID: 1971232

Cluster

View cluster (26 members)

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 15-146
PDB
Domain cluster: rep: IMGVR_UViG_3300030493_000399-3300030493-Ga0310040_100013118__D1-105
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 40.5 3.60e-10 99.2% 68.6%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4a8eA02 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.86 74.0 6.54e-01 100.0% 65.9%
1aihA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.84 62.0 5.59e-01 100.0% 58.2%
4acoA02 1.10.443.20 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Centromere DNA-binding protein complex CBF3 subunit, domain 2 0.74 69.0 4.99e-01 100.0% 48.8%
3sqiA02 1.10.443.20 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Centromere DNA-binding protein complex CBF3 subunit, domain 2 0.70 65.0 4.96e-01 100.0% 54.9%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 28.0 3.24e-01 93.9% 64.9%
1y5lA02 3.40.50.12440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 40.0 2.36e-01 79.5% 68.1%
5eriA00 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 0.52 39.0 3.75e-01 100.0% 68.0%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4122043 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.94 80.0 8.42e-01 100.0% 96.7%
4981577 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.90 76.0 7.82e-01 100.0% 92.0%
4966682 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.90 75.0 8.06e-01 99.2% 99.1%
5058465 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.90 74.0 7.59e-01 100.0% 89.6%
4637388 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.90 71.0 6.42e-01 100.0% 63.5%
5029991 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.89 75.0 7.69e-01 100.0% 91.2%
4314510 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.89 69.0 7.59e-01 98.5% 96.4%
4930303 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.89 71.0 7.58e-01 100.0% 94.8%
4973226 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.88 72.0 7.61e-01 100.0% 93.3%
4975762 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.88 75.0 7.75e-01 100.0% 93.6%
5052541 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.87 75.0 7.78e-01 100.0% 94.4%
3590887 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.87 83.0 8.17e-01 100.0% 96.4%
4936284 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.87 70.0 7.50e-01 100.0% 95.7%
4285602 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.86 75.0 7.55e-01 100.0% 91.5%
4933965 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.85 73.0 7.56e-01 98.5% 94.4%
5059725 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.85 72.0 6.36e-01 100.0% 64.4%
4929009 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.84 75.0 7.62e-01 100.0% 94.6%
4932090 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.83 73.0 7.49e-01 100.0% 96.0%
5018485 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.81 77.0 6.98e-01 100.0% 92.4%
4093657 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.81 72.0 7.15e-01 100.0% 91.1%
5007182 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.80 62.0 5.82e-01 100.0% 67.7%
3199994 101.1.8.10 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › DUF3435 0.80 75.0 6.00e-01 100.0% 80.8%
5016957 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.80 75.0 6.75e-01 100.0% 76.0%
3589779 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.79 76.0 7.19e-01 100.0% 96.0%
4253165 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.77 70.0 6.90e-01 100.0% 91.4%
4940634 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.70 66.0 6.41e-01 100.0% 93.1%
D2 medium residues 147-208
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 29.4 9.00e-07 80.7% 25.0%
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rn7A01 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 0.71 52.0 5.09e-01 77.4% 75.8%
1ignB02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.70 49.0 4.37e-01 75.8% 53.3%
1ug2A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.69 49.0 5.22e-01 77.4% 90.4%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.68 58.0 4.41e-01 98.4% 100.0%
7z7vE01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.64 44.0 4.54e-01 72.6% 78.3%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.64 55.0 4.65e-01 96.8% 75.5%
2gloA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.64 43.0 4.45e-01 75.8% 74.6%
1vf6C00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.61 36.0 3.94e-01 72.6% 70.6%
5z62E00 1.25.40.40 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI 0.57 44.0 3.73e-01 85.5% 83.5%
1m6yA02 1.10.150.170 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative methyltransferase TM0872, insert domain 0.57 43.0 3.72e-01 83.9% 66.7%
4a18Q01 1.10.10.1760 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ribosomal protein L36 0.57 41.0 4.04e-01 80.6% 78.3%
1r4aE00 1.10.220.60 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › GRIP domain 0.56 36.0 3.92e-01 80.6% 80.4%
3eyyA01 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 0.56 45.0 4.18e-01 93.5% 75.6%
4eqqA02 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 0.56 40.0 4.28e-01 77.4% 100.0%
3pasA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 45.0 3.34e-01 100.0% 80.0%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 42.0 3.65e-01 90.3% 88.0%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.54 41.0 3.89e-01 88.7% 71.6%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 37.0 3.52e-01 75.8% 60.3%
4l7mA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.53 42.0 2.84e-01 91.9% 62.1%
2hqtK00 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 42.0 3.52e-01 95.2% 82.9%
7wu8B01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.51 38.0 3.65e-01 87.1% 79.7%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 40.0 3.74e-01 90.3% 71.8%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4031830 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.89 67.0 7.50e-01 88.7% 98.0%
4981564 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.79 64.0 6.82e-01 93.5% 98.2%
4927068 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.78 57.0 6.05e-01 88.7% 87.3%
2417767 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.78 56.0 5.75e-01 93.5% 79.7%
4194508 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.78 59.0 6.21e-01 91.9% 89.1%
4608916 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.77 56.0 5.93e-01 90.3% 85.5%
4390290 101.1.1.13 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_1 0.72 54.0 5.36e-01 80.6% 87.7%
3672635 101.1.1.295 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_70 0.70 53.0 5.03e-01 82.3% 72.0%
3800383 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.69 52.0 5.20e-01 82.3% 78.5%
3856707 101.1.1.89 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding_7 0.69 52.0 4.89e-01 80.6% 66.7%
3692197 101.1.3.9 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › Myb_DNA-bind_8 0.68 48.0 5.25e-01 75.8% 98.0%
4027285 101.1.1.3 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding 0.65 47.0 4.27e-01 77.4% 56.5%
4122129 2008.1.1.93 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › TPD 0.61 47.0 3.48e-01 88.7% 30.3%
3700138 574.1.1.1 ↗ alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp 0.59 45.0 4.40e-01 85.5% 85.7%
3493041 3796.1.1.2 ↗ alpha arrays › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › GRIP 0.59 43.0 4.38e-01 80.6% 86.2%
5025549 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 40.0 3.99e-01 77.4% 87.7%
5037841 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.56 46.0 3.94e-01 98.4% 52.2%
3196401 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 41.0 4.24e-01 87.1% 94.5%
3647237 611.3.1.0 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.52 40.0 3.41e-01 91.9% 57.5%
1503553 3796.1.1.1 ↗ alpha arrays › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Isd_H_B_linker 0.50 40.0 3.74e-01 90.3% 71.8%