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MN234216.1__QFG13224.1__SEA_GILGAMESH_32__00032

Bact-Vir

MN234216.1__QFG13224.1__SEA_GILGAMESH_32__00032

Identity

Accession:
MN234216 ↗
Kingdom:
phage

Quality

85.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gilgameshvirus› Streptomyces_phage_Gilgamesh

TaxID: 2599890

Cluster

View cluster (138 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 75-156
PDB
Domain cluster: representative
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4acoA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.78 69.0 6.28e-01 97.6% 97.3%
2a3vB01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.77 67.0 6.36e-01 91.5% 91.5%
4a8eA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.75 60.0 5.90e-01 84.1% 95.4%
2klqA00 1.20.58.870 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 49.0 4.34e-01 72.0% 65.8%
2x48A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 40.0 4.81e-01 84.1% 92.6%
3ztaA00 1.10.490.130 Mainly Alpha › Orthogonal Bundle › Globin-like › 0.66 56.0 4.78e-01 96.3% 88.5%
1td6A01 1.20.1480.10 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › hypothetical protein mp506/mpn330, domain 1 0.62 43.0 4.08e-01 76.8% 58.8%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.62 53.0 5.21e-01 97.6% 95.5%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 4.08e-01 75.6% 87.0%
4h3tA02 1.10.132.100 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.61 47.0 3.89e-01 81.7% 83.0%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.60 46.0 4.62e-01 84.1% 93.8%
1t7lB01 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.59 49.0 3.28e-01 96.3% 34.7%
1zvwA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.59 43.0 4.73e-01 78.0% 98.5%
4cvnA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 48.0 3.82e-01 92.7% 96.6%
5uidA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.58 45.0 3.21e-01 92.7% 27.9%
2vixA03 1.20.1280.240 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.58 49.0 4.52e-01 98.8% 89.4%
2gomA00 1.10.10.1270 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Sbi, C3 binding domain IV 0.57 40.0 4.52e-01 97.6% 100.0%
2olpA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 47.0 3.96e-01 93.9% 83.4%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.57 47.0 3.85e-01 97.6% 54.0%
4ga4A01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.57 42.0 4.58e-01 84.1% 97.0%
1b0bA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 48.0 4.11e-01 98.8% 84.4%
2es9A00 1.20.1290.30 Mainly Alpha › Up-down Bundle › AhpD-like › 0.56 44.0 4.16e-01 86.6% 73.0%
1x46A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.55 48.0 4.01e-01 98.8% 82.0%
3h5qA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.55 42.0 4.50e-01 84.1% 97.1%
2cwyA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.55 43.0 4.14e-01 86.6% 79.6%
3rc3A02 1.20.272.40 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.55 44.0 4.38e-01 95.1% 86.2%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.55 47.0 4.46e-01 95.1% 81.4%
4eadA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.54 44.0 4.08e-01 90.2% 71.0%
5dikA00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.54 46.0 4.21e-01 98.8% 81.2%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.53 39.0 3.95e-01 81.7% 87.1%
2vqgA00 1.10.10.1280 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Alpha-helical porin B/porin C 0.53 38.0 3.91e-01 75.6% 96.1%
2oifB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 43.0 3.66e-01 93.9% 83.4%
1r3dA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 45.0 3.23e-01 96.3% 72.0%
3qnfA04 1.10.3480.20 Mainly Alpha › Orthogonal Bundle › TorD-like › 0.53 44.0 3.56e-01 97.6% 93.2%
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 0.52 38.0 4.04e-01 79.3% 95.8%
5lb3B02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 41.0 3.08e-01 91.5% 81.6%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3289283 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.91 82.0 6.71e-01 96.3% 92.9%
4303782 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.89 79.0 6.86e-01 95.1% 96.7%
2095887 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.88 81.0 7.03e-01 98.8% 100.0%
4169335 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.83 69.0 6.44e-01 87.8% 97.0%
4396981 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.82 69.0 6.37e-01 87.8% 96.0%
4566333 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.81 68.0 6.28e-01 87.8% 97.0%
4579981 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.77 70.0 6.22e-01 96.3% 91.8%
4063794 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.77 66.0 5.91e-01 91.5% 90.9%
4947439 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.76 66.0 6.40e-01 91.5% 97.8%
4964250 186.1.1.4 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_4 0.76 65.0 5.76e-01 91.5% 87.8%
5004327 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.71 66.0 5.77e-01 97.6% 90.4%
5081313 182.1.3.0 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.69 51.0 4.97e-01 78.0% 75.6%
4959042 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.69 63.0 5.79e-01 100.0% 83.8%
2491401 109.51.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › TssA helical domains › TssA helical domains › ImpA_N 0.65 55.0 3.99e-01 96.3% 93.4%
4025031 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.63 49.0 3.82e-01 85.4% 45.3%
5083505 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.63 57.0 5.44e-01 100.0% 92.6%
3795092 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.62 44.0 3.79e-01 75.6% 83.0%
5057633 3651.1.1.0 ↗ alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain 0.62 47.0 4.25e-01 85.4% 59.1%
3464434 180.1.1.1 ↗ alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2 0.60 47.0 3.78e-01 85.4% 80.6%
3379044 109.3.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank 0.60 52.0 3.54e-01 96.3% 43.4%
3390844 109.4.1.27 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › W2 0.59 51.0 4.10e-01 97.6% 48.5%
3621977 3198.1.1.1 ↗ alpha bundles › ABA-1 repeat unit › ABA-1 repeat unit › ABA-1 repeat unit › NPA 0.59 45.0 4.08e-01 84.1% 100.0%
3877071 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.59 43.0 3.44e-01 79.3% 70.9%
4958049 4204.1.1.5 ↗ alpha bundles › AF0941-like › AF0941-like › AF0941-like › DUF2150 0.59 45.0 4.18e-01 85.4% 100.0%
145202 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.58 48.0 4.02e-01 93.9% 83.4%
5024540 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.57 41.0 3.48e-01 78.0% 70.3%
3247705 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.56 46.0 3.31e-01 95.1% 86.8%
3289554 106.1.1.11 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N 0.56 46.0 4.18e-01 95.1% 92.5%
3391 138.1.1.11 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › RFC_C 0.55 47.0 4.43e-01 95.1% 79.8%
3502846 109.4.1.27 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › W2 0.55 45.0 3.69e-01 97.6% 54.6%
3540760 633.21.1.10 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › MARVEL 0.54 41.0 3.44e-01 84.1% 80.6%
D2 high residues 166-336
PDB
Domain cluster: rep: IMGVR_UViG_3300009506_002638-3300009506-Ga0118657_1006709312__D23-176
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 33.3 5.90e-08 98.2% 77.3%
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1f44A01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.85 75.0 7.17e-01 100.0% 80.9%
5jk0B01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.84 68.0 6.84e-01 100.0% 83.2%
1ae9A00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.80 65.0 6.50e-01 100.0% 83.6%
2h7fX02 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.73 58.0 5.11e-01 100.0% 58.5%
3m4aA03 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.73 50.0 5.91e-01 83.6% 100.0%
4acoA02 1.10.443.20 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Centromere DNA-binding protein complex CBF3 subunit, domain 2 0.70 66.0 5.17e-01 100.0% 65.8%
2a3vA02 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.69 65.0 5.99e-01 100.0% 82.5%
2v6eA03 1.10.443.30 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Telomere resolvase 0.62 54.0 4.95e-01 100.0% 71.6%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3943512 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.91 67.0 7.53e-01 90.6% 94.8%
4101478 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.91 72.0 7.86e-01 90.1% 95.9%
5057283 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.89 62.0 7.02e-01 90.6% 89.6%
5072041 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.89 60.0 6.90e-01 90.6% 90.0%
5059725 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.88 68.0 6.65e-01 100.0% 74.4%
4118349 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.88 60.0 6.78e-01 90.1% 88.1%
4929009 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.86 62.0 7.05e-01 90.1% 95.4%
4960057 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.86 62.0 6.89e-01 90.1% 90.0%
5003452 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.86 62.0 7.15e-01 90.6% 97.7%
5027341 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.85 62.0 6.40e-01 100.0% 78.8%
4453818 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.85 68.0 7.32e-01 97.7% 94.7%
4463631 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.84 63.0 7.05e-01 91.2% 97.0%
3839627 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.84 60.0 6.77e-01 90.1% 93.3%
3958910 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.83 62.0 6.84e-01 90.1% 92.9%
5073434 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.82 72.0 6.75e-01 100.0% 77.0%
5052502 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.82 60.0 6.76e-01 90.1% 94.8%
4112553 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.82 62.0 6.73e-01 90.1% 91.0%
3271483 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.81 73.0 7.03e-01 100.0% 84.2%
3946063 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.81 65.0 6.23e-01 100.0% 73.3%
3251731 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.80 65.0 6.83e-01 90.6% 92.9%
4964815 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.79 65.0 6.92e-01 91.8% 96.0%
4046017 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.79 63.0 6.79e-01 91.8% 96.6%
4966027 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.78 60.0 5.85e-01 100.0% 73.9%
3926774 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.77 60.0 6.63e-01 87.1% 97.9%
3839222 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.77 57.0 6.30e-01 91.2% 93.6%
5002702 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.75 69.0 6.65e-01 100.0% 85.8%
4940211 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.75 69.0 6.96e-01 100.0% 95.9%
3589779 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.74 61.0 6.49e-01 90.6% 96.7%
4964439 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.74 70.0 6.44e-01 100.0% 90.2%
4556095 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.73 60.0 6.51e-01 90.1% 100.0%
4938259 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.72 59.0 6.38e-01 86.0% 99.3%
3494533 101.1.8.12 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › DUF3504 0.72 60.0 6.25e-01 96.5% 93.8%
4965169 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.72 68.0 6.29e-01 100.0% 84.3%
4928148 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.64 57.0 5.83e-01 100.0% 95.2%
3291724 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.63 31.0 4.20e-01 91.8% 88.9%
3727612 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.62 47.0 4.68e-01 78.9% 91.7%