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NC_054726.1__YP_010059669.1__KHQ86_gp106__00193

Bact-Vir

NC_054726.1__YP_010059669.1__KHQ86_gp106__00193

Identity

Accession:
NC_054726 ↗
Kingdom:
phage

Quality

58.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stormageddonvirus› Gordonia_phage_Stormageddon

TaxID: 2656541

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 99-172
PDB
Domain cluster: rep: NC_054726.1__YP_010059639.1__KHQ86_gp136__00163__D59-136
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05305.20 best DUF732 38.7 1.60e-09 98.7% 98.6%
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.74 65.0 5.88e-01 100.0% 73.2%
1u3dA03 1.10.579.10 Mainly Alpha › Orthogonal Bundle › DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 › DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 0.74 54.0 3.99e-01 78.4% 67.9%
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 0.73 51.0 5.34e-01 82.4% 81.8%
4ad9A02 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 0.72 52.0 5.00e-01 75.7% 76.2%
2r0qC02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.70 48.0 5.49e-01 90.5% 96.4%
3fblA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 60.0 5.88e-01 98.6% 97.6%
1x4qA01 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.68 50.0 5.14e-01 98.6% 83.1%
4ye6A02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.67 49.0 5.42e-01 77.0% 100.0%
3d7iB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.67 46.0 4.16e-01 70.3% 53.1%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 53.0 5.21e-01 94.6% 80.8%
7ccmB01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.66 52.0 4.21e-01 86.5% 49.0%
1ug2A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 43.0 4.86e-01 77.0% 96.2%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.66 51.0 4.69e-01 100.0% 64.9%
2x3mA00 1.25.40.670 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 57.0 4.46e-01 100.0% 56.6%
7p2yd01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.64 54.0 5.00e-01 95.9% 81.8%
6fakA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.64 47.0 4.61e-01 78.4% 71.6%
3ubcA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 54.0 4.57e-01 100.0% 73.3%
5oklA01 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.61 46.0 4.22e-01 82.4% 85.1%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.61 44.0 4.02e-01 74.3% 74.2%
1kxpD04 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.61 43.0 4.26e-01 74.3% 76.6%
4jd9G00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.61 46.0 3.98e-01 82.4% 60.8%
2w9zA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.60 51.0 4.28e-01 98.6% 53.4%
1kxpD02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.60 44.0 4.18e-01 78.4% 69.3%
1xriA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.60 52.0 4.18e-01 98.6% 73.5%
4fqnC00 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.58 44.0 4.29e-01 91.9% 72.9%
1m70A02 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.58 47.0 4.30e-01 89.2% 90.9%
3v53E00 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.58 45.0 4.15e-01 97.3% 63.7%
3b0pA02 1.20.120.1460 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 39.0 3.91e-01 73.0% 78.7%
2k8oA00 1.20.5.2120 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.56 31.0 3.39e-01 75.7% 65.0%
2prrA02 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.55 48.0 4.05e-01 98.6% 76.4%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.55 43.0 4.35e-01 87.8% 93.3%
2i53A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.54 44.0 3.93e-01 98.6% 61.3%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.54 38.0 3.43e-01 74.3% 99.1%
1zcdA00 1.20.1530.10 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain 0.53 39.0 2.59e-01 81.1% 18.1%
3ezhA00 1.20.120.960 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase NarX, sensor domain 0.52 37.0 3.26e-01 75.7% 78.9%
2hfiA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.52 38.0 3.20e-01 75.7% 80.5%
1s35A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 37.0 3.32e-01 77.0% 88.1%
1biqA00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.50 38.0 2.52e-01 82.4% 32.9%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3954237 532.2.1.16 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains › DUF732 0.93 85.0 8.29e-01 100.0% 90.0%
4942265 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.91 63.0 6.00e-01 71.6% 77.6%
3955500 101.1.2.655 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF732 0.89 81.0 7.94e-01 100.0% 92.3%
3291410 592.2.1.0 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like 0.84 75.0 7.52e-01 95.9% 100.0%
4501343 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.82 58.0 6.57e-01 77.0% 100.0%
4944767 101.1.2.883 ↗ alpha arrays › HTH › HTH › winged helix domain › Radical_SAM 0.81 56.0 5.66e-01 71.6% 82.7%
4167899 7000.1.1.0 ↗ alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.81 52.0 5.92e-01 73.0% 89.1%
4927804 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.78 54.0 5.43e-01 95.9% 70.7%
3992048 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.78 54.0 6.10e-01 81.1% 98.2%
3672635 101.1.1.295 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_70 0.78 60.0 6.04e-01 82.4% 82.7%
3724068 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.77 55.0 6.13e-01 85.1% 100.0%
4951565 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.77 61.0 4.56e-01 100.0% 35.6%
4499345 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.75 49.0 5.80e-01 78.4% 100.0%
4436111 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.75 67.0 4.71e-01 100.0% 33.9%
3742738 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.74 52.0 4.35e-01 73.0% 69.6%
1566530 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.74 55.0 5.35e-01 78.4% 80.2%
4978129 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.73 50.0 3.13e-01 71.6% 16.1%
5067688 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.73 54.0 5.61e-01 98.6% 82.9%
4969467 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 58.0 5.20e-01 100.0% 61.9%
167309 592.2.1.3 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like › Nab2 0.73 63.0 5.60e-01 100.0% 67.6%
3928773 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.72 59.0 5.91e-01 98.6% 89.3%
4506746 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.72 51.0 3.77e-01 74.3% 64.2%
4957643 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.72 60.0 4.10e-01 91.9% 52.1%
4034503 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.72 53.0 5.65e-01 98.6% 90.8%
3966077 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.71 57.0 5.90e-01 98.6% 92.9%
5026098 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.70 59.0 4.33e-01 100.0% 35.0%
5045542 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.68 55.0 4.11e-01 100.0% 34.0%
3800383 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.68 53.0 5.61e-01 89.2% 98.5%
5006976 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 58.0 4.46e-01 95.9% 44.5%
5074415 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.67 56.0 4.24e-01 100.0% 38.4%
3288392 608.1.1.1 ↗ alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.66 46.0 3.94e-01 71.6% 46.1%
4390290 101.1.1.13 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_1 0.66 48.0 5.09e-01 81.1% 89.2%
3839043 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.65 55.0 4.19e-01 97.3% 49.2%
5025549 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 46.0 4.86e-01 77.0% 96.9%
3253015 6088.1.1.2 ↗ alpha arrays › Helical bundle domain in elongation factor 3A › Helical bundle domain in elongation factor 3A › Helical bundle domain in elongation factor 3A › PF26051 0.64 53.0 5.25e-01 97.3% 95.0%
3957626 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.63 54.0 4.43e-01 100.0% 54.0%
4531271 101.1.2.498 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25870 0.63 52.0 4.20e-01 93.2% 58.0%
5048289 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.63 53.0 4.04e-01 98.6% 45.3%
3740124 101.1.17.19 ↗ alpha arrays › HTH › HTH › FF domain › DEK_C 0.62 44.0 4.80e-01 82.4% 100.0%
3240014 138.1.1.0 ↗ 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 0.62 42.0 3.93e-01 70.3% 56.4%
4972840 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.62 54.0 4.00e-01 100.0% 41.0%
3847014 3919.1.1.2 ↗ alpha duplicates or obligate multimers › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › COMM_HN 0.62 53.0 4.61e-01 95.9% 95.7%
3176271 2007.2.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase2 0.62 55.0 4.02e-01 98.6% 45.1%
4953264 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.61 48.0 4.58e-01 83.8% 78.8%
4434935 195.1.1.1 ↗ alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.60 52.0 4.30e-01 100.0% 55.0%
None — 0.60 53.0 4.10e-01 98.6% 66.9%
3889216 509.1.1.3 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › USH1C_N 0.57 44.0 4.45e-01 100.0% 88.0%
5004327 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.56 42.0 3.77e-01 83.8% 80.9%
4929245 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.54 42.0 4.30e-01 87.8% 92.9%
5080068 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.54 45.0 4.22e-01 100.0% 79.0%
3464273 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.52 35.0 3.04e-01 70.3% 78.3%
None — 0.51 40.0 2.60e-01 85.1% 66.2%
3221554 4218.1.1.1 ↗ alpha bundles › TAFH domain-like › TAFH domain-like › TAFH domain-like › TAFH 0.50 42.0 3.98e-01 98.6% 87.4%
D2 medium residues 1-54
PDB