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NC_041929.1__YP_009601413.1__FDH46_gp190__00288

Bact-Vir

NC_041929.1__YP_009601413.1__FDH46_gp190__00288

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

76.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 17-82
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.70 50.0 3.83e-01 81.8% 34.0%
2c42A06 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.68 56.0 3.42e-01 87.9% 21.6%
1k8kG00 1.25.40.190 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Actin-related protein 2/3 complex subunit 5 0.67 50.0 3.95e-01 80.3% 38.1%
3d7iB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.67 47.0 4.16e-01 74.2% 51.0%
2vkjA00 1.20.58.2030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 45.0 3.88e-01 97.0% 43.4%
2yjgA01 3.90.226.30 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › LarA, C-terminal domain 0.67 53.0 3.81e-01 86.4% 45.4%
4rg9B04 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.65 47.0 4.20e-01 78.8% 83.3%
4gczA03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.64 43.0 4.39e-01 90.9% 70.8%
3tl4X02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.64 52.0 5.09e-01 89.4% 90.3%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 48.0 4.24e-01 92.4% 56.2%
4ciuA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 51.0 3.57e-01 90.9% 30.2%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.61 46.0 4.69e-01 86.4% 98.4%
2mqkA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.60 36.0 3.63e-01 80.3% 58.5%
2efjA01 1.10.1200.270 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Methyltransferase, alpha-helical capping domain 0.60 40.0 3.14e-01 77.3% 33.6%
1k07A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.60 40.0 2.75e-01 75.8% 17.6%
4wu0A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.59 51.0 3.24e-01 100.0% 84.7%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.59 54.0 4.66e-01 100.0% 88.9%
2gl2B00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 50.0 4.16e-01 90.9% 67.0%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.59 48.0 4.25e-01 89.4% 81.2%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.59 48.0 4.46e-01 89.4% 71.2%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.58 51.0 4.38e-01 98.5% 66.7%
3ibpA01 1.20.58.850 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 49.0 4.76e-01 90.9% 90.3%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 49.0 3.87e-01 95.5% 93.3%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.55 48.0 4.56e-01 98.5% 98.7%
3g2eB00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.54 43.0 3.13e-01 87.9% 33.0%
1eteA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.51 37.0 3.08e-01 81.8% 55.2%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3248091 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.73 59.0 5.37e-01 86.4% 72.9%
223985 3600.1.1.1 ↗ alpha bundles › uncharacterized protein SYNW0670 › uncharacterized protein SYNW0670 › uncharacterized protein SYNW0670 › YlqD 0.70 50.0 3.84e-01 81.8% 34.2%
5001590 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.66 52.0 5.73e-01 86.4% 100.0%
4978829 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.66 51.0 5.03e-01 86.4% 77.1%
3589720 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.66 48.0 3.69e-01 90.9% 34.5%
3400926 3758.1.1.45 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › Not3 0.66 52.0 4.26e-01 83.3% 57.4%
4499345 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 44.0 4.85e-01 78.8% 92.0%
5059135 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.63 50.0 4.93e-01 83.3% 91.4%
5051215 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.63 55.0 5.30e-01 98.5% 89.3%
3167298 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.63 51.0 4.30e-01 86.4% 57.1%
5014267 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.62 50.0 4.91e-01 84.8% 94.3%
5060023 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.60 48.0 4.73e-01 84.8% 92.9%
3215342 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.60 48.0 4.18e-01 87.9% 58.9%
4286197 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.59 48.0 4.46e-01 86.4% 90.0%
1266295 247.1.1.0 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase 0.58 50.0 3.34e-01 100.0% 26.0%
5057549 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 48.0 3.87e-01 89.4% 50.8%
4971151 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.56 42.0 3.09e-01 80.3% 29.8%
2073547 621.1.1.2 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Smg8_Smg9 0.56 48.0 4.83e-01 98.5% 100.0%
4439831 2004.1.1.193 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_19 0.52 44.0 2.97e-01 97.0% 63.3%
4959075 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.51 41.0 2.67e-01 100.0% 16.9%