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NC_042062.1__YP_009617830.1__QII00_sAgp01__00001

Bact-Vir

NC_042062.1__YP_009617830.1__QII00_sAgp01__00001

Identity

Accession:
NC_042062 ↗
Kingdom:
phage

Quality

76.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nonanavirus› Salmonella_phage_SP069

TaxID: 1173760

Cluster

View cluster (4 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 10-97
PDB
Domain cluster: rep: OX241556.1__CAH9016388.1__VP141E351_P0091__00091__D7-88
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cmpA00 1.10.10.1400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Terminase, small subunit, N-terminal DNA-binding domain, HTH motif 0.91 57.0 7.15e-01 70.5% 100.0%
3vfzB00 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 46.0 5.32e-01 79.5% 90.5%
4nqwA02 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 45.0 5.12e-01 76.1% 89.1%
5xsoA02 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 0.70 50.0 5.37e-01 85.2% 86.8%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.68 37.0 3.52e-01 100.0% 43.9%
5ow2A00 1.10.10.930 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.68 43.0 4.68e-01 81.8% 78.1%
3hugA00 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 0.61 42.0 4.34e-01 76.1% 77.5%
1stzA01 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 0.60 42.0 4.31e-01 73.9% 84.7%
2f1kC02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.59 48.0 4.45e-01 87.5% 80.5%
6v3zA00 1.20.141.10 Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1 0.59 40.0 3.12e-01 80.7% 33.7%
3b1fA02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.59 47.0 4.39e-01 86.4% 79.3%
1s7oB00 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 44.0 4.24e-01 98.9% 71.4%
4h03A02 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.57 45.0 3.43e-01 85.2% 77.2%
1f45B00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 39.0 3.45e-01 100.0% 49.6%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 40.0 3.18e-01 77.3% 40.8%
6hxpA01 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.54 37.0 3.59e-01 71.6% 100.0%
2e8gA01 1.20.1440.150 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.54 37.0 3.42e-01 97.7% 52.4%
1r4wA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 39.0 2.99e-01 77.3% 44.7%
3vprA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 42.0 3.57e-01 85.2% 60.7%
2mqkA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.51 29.0 3.19e-01 71.6% 69.2%
2b5uA02 1.10.287.620 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix Hairpins 0.51 38.0 3.14e-01 80.7% 43.5%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4602544 138.1.1.9 ↗ 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 › DNA_pol3_delta_C 0.72 47.0 4.11e-01 84.1% 46.4%
3168260 3911.1.1.1 ↗ extended segments › Exosome complex protein LRP1 › Exosome complex protein LRP1 › Exosome complex protein LRP1 › Sas10_Utp3 0.68 39.0 3.51e-01 93.2% 41.7%
3283074 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.67 50.0 5.15e-01 85.2% 81.2%
3975610 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.65 44.0 4.84e-01 80.7% 87.1%
3714592 189.1.1.0 ↗ alpha bundles › GTPase activation domain, GAP › GTPase activation domain, GAP › GTPase activation domain, GAP 0.63 45.0 3.18e-01 75.0% 85.4%
3256832 3881.1.1.0 ↗ alpha bundles › CNOT9 binding domain CN9BD (DUF3819) › CNOT9 binding domain CN9BD (DUF3819) › CNOT9 binding domain CN9BD (DUF3819) 0.63 51.0 3.95e-01 89.8% 79.0%
3280686 101.1.3.4 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › HTH_30 0.60 46.0 4.40e-01 85.2% 72.0%
3938660 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.59 49.0 3.37e-01 100.0% 25.5%
3512259 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.58 42.0 4.08e-01 80.7% 87.6%
3600676 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.57 41.0 3.87e-01 84.1% 60.9%
3804219 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.54 42.0 4.22e-01 100.0% 82.2%
3847817 109.25.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › GPCR-autoproteolysis inducing domain subdomain A › GPCR-autoproteolysis inducing domain subdomain A › GAIN 0.54 36.0 3.30e-01 73.9% 52.2%
3290011 3843.1.1.4 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.53 35.0 3.43e-01 88.6% 61.1%
3969000 5060.2.1.1 ↗ alpha bundles › V-type ATP synthase subunit C › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › T2SSF 0.52 40.0 3.66e-01 81.8% 77.4%
4967859 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 42.0 3.90e-01 89.8% 87.0%
3925867 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.50 46.0 2.97e-01 100.0% 40.8%
4433130 106.1.1.7 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Protoglobin 0.50 45.0 3.68e-01 100.0% 97.6%
D2 high residues 102-158
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o8bA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.58 47.0 4.29e-01 96.5% 71.1%
1wxnA00 2.20.20.10 Mainly Beta › Single Sheet › Anthopleurin-A › Anthopleurin-A 0.56 38.0 4.16e-01 82.5% 95.2%
4c23B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 39.0 2.65e-01 75.4% 22.6%
4pphA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.56 46.0 3.31e-01 100.0% 33.3%
4pioA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 40.0 2.99e-01 82.5% 95.6%
2p1gA02 2.30.260.10 Mainly Beta › Roll › putative xylanase like fold › putative xylanase like domain 0.55 47.0 3.99e-01 100.0% 98.0%
1aorA02 1.10.569.10 Mainly Alpha › Orthogonal Bundle › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 0.55 40.0 2.90e-01 82.5% 50.0%
6ko5A02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 37.0 2.49e-01 82.5% 67.5%
4bfmA00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.51 40.0 2.61e-01 91.2% 42.5%
4apmA03 2.60.40.4360 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 39.0 3.97e-01 86.0% 84.2%
4m9fA00 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.51 41.0 2.97e-01 100.0% 89.0%
1zvpD00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.51 38.0 3.07e-01 87.7% 77.9%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.50 35.0 3.40e-01 100.0% 63.8%
7q5yB01 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.50 40.0 3.37e-01 100.0% 65.8%
2dr1A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.50 41.0 3.28e-01 100.0% 49.6%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3636393 304.8.1.6 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_3 0.59 37.0 3.76e-01 100.0% 63.6%
4124613 2484.1.1.175 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N+FGGY_C 0.58 41.0 2.44e-01 77.2% 12.0%
3664981 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.56 34.0 3.90e-01 87.7% 89.7%
4025692 601.23.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.56 47.0 2.98e-01 100.0% 20.6%
4329083 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 42.0 2.74e-01 89.5% 43.2%
4252702 601.23.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.55 44.0 2.89e-01 96.5% 18.7%
3377898 4.8.1.32 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_PTM 0.54 46.0 4.06e-01 100.0% 80.0%
4624584 601.23.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.54 44.0 2.88e-01 98.2% 18.4%
3914004 316.1.1.6 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Mab-21 0.53 43.0 2.89e-01 100.0% 22.1%
4015812 387.1.1.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.53 33.0 3.72e-01 98.2% 100.0%
5047964 242.4.1.2 ↗ a+b two layers › Homing endonucleases-like › DNA polymerase II large subunit DP2 central a+b domain › DNA polymerase II large subunit DP2 central a+b domain › PolC_DP2_central 0.52 42.0 3.61e-01 100.0% 62.9%
1843010 331.19.1.1 ↗ a+b two layers › TBP-like › Toxin RnlA N-terminal domains › Toxin RnlA N-terminal domains › RnlA_toxin 0.51 35.0 3.26e-01 73.7% 73.8%
3718563 243.6.1.0 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain 0.50 33.0 3.27e-01 100.0% 63.3%
3994458 389.1.1.0 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin 0.50 32.0 3.04e-01 96.5% 52.2%
D3 high residues 167-215
PDB