Back to structures

NC_031005.2__YP_009278007.1__SEA_QUEENBEY_29__00029

Bact-Vir

NC_031005.2__YP_009278007.1__SEA_QUEENBEY_29__00029

Identity

Accession:
NC_031005 ↗
Kingdom:
phage

Quality

81.2 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 17-79
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23817.2 best DUF7188 140.8 6.10e-41 100.0% 33.7%
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4evfA01 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.70 60.0 5.79e-01 95.2% 98.6%
4f3fC00 1.20.970.40 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › 0.69 50.0 5.19e-01 90.5% 84.7%
1f5oA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.69 59.0 4.58e-01 100.0% 51.0%
1h97A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.68 60.0 4.57e-01 100.0% 55.1%
2x3mA00 1.25.40.670 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.66 57.0 4.29e-01 100.0% 40.4%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.66 55.0 4.31e-01 100.0% 77.2%
2wy4A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.65 56.0 4.42e-01 100.0% 68.3%
1z21A00 1.10.10.1000 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Type III secretion system virulence factor YopR, core domain 0.64 56.0 4.90e-01 100.0% 76.0%
7shlA02 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.64 51.0 4.21e-01 92.1% 82.8%
1oj6A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 53.0 4.18e-01 100.0% 57.1%
4eadA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.63 53.0 4.58e-01 100.0% 68.2%
2jpnA00 1.20.1280.210 Mainly Alpha › Up-down Bundle › Monooxygenase › Uncharacterised protein UvsW.1 0.63 46.0 4.32e-01 79.4% 67.1%
4gtnA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.62 52.0 5.00e-01 96.8% 87.8%
1khdA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.60 49.0 4.36e-01 100.0% 72.0%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.59 45.0 3.80e-01 84.1% 84.8%
2l3lA01 1.20.58.1250 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Tubulin Binding Cofactor C, N-terminal domain 0.59 45.0 3.84e-01 84.1% 62.3%
3iuoA00 1.10.10.1390 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › ATP-dependent DNA helicase RecQ 0.59 46.0 3.97e-01 90.5% 87.2%
1n81A00 1.10.3030.10 Mainly Alpha › Orthogonal Bundle › Gametocyte protein Pfg27 › Gametocyte protein Pfg27 0.58 44.0 3.19e-01 82.5% 37.6%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.58 48.0 4.35e-01 92.1% 86.4%
1mhyG02 1.20.1280.30 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 2 0.58 46.0 4.38e-01 85.7% 89.0%
2raaA00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.58 41.0 3.05e-01 77.8% 29.2%
1gzsB00 1.10.4120.10 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › SopE-like, GEF domain 0.57 44.0 3.28e-01 84.1% 75.2%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 43.0 3.62e-01 82.5% 84.0%
3k9iA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 48.0 4.09e-01 93.7% 57.3%
3ab3D00 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.56 45.0 3.45e-01 93.7% 82.4%
2pftA00 1.20.1280.170 Mainly Alpha › Up-down Bundle › Monooxygenase › Exocyst complex component Exo70 0.56 46.0 2.80e-01 100.0% 32.9%
1eyvB00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.56 47.0 3.81e-01 100.0% 99.2%
3mvpA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 46.0 3.67e-01 100.0% 80.5%
4muoA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.56 44.0 4.33e-01 93.7% 84.7%
2xs1A01 1.25.40.280 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › alix/aip1 like domains 0.55 47.0 2.93e-01 95.2% 63.0%
6fdpA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 47.0 3.80e-01 96.8% 50.8%
3s6jE02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 37.0 3.61e-01 71.4% 78.3%
1t3qA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.54 38.0 3.54e-01 76.2% 69.1%
3gw4A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 46.0 3.28e-01 96.8% 35.4%
2klqA00 1.20.58.870 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 41.0 3.49e-01 85.7% 82.5%
2dsjA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.53 42.0 4.14e-01 90.5% 95.5%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 45.0 4.26e-01 93.7% 85.3%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.52 38.0 3.73e-01 77.8% 73.1%
1sk7A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.52 46.0 3.32e-01 100.0% 61.5%
1r3dA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 2.85e-01 92.1% 68.9%
4ga4A01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.51 41.0 4.07e-01 95.2% 92.5%
1cnt200 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.50 37.0 3.01e-01 81.0% 50.0%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.50 39.0 3.67e-01 87.3% 82.7%
2i6hA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 43.0 3.76e-01 98.4% 63.5%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3378713 226.1.1.0 a+b two layers › POZ domain › POZ domain › POZ domain 0.70 57.0 4.34e-01 100.0% 37.4%
3233038 226.1.1.41 a+b two layers › POZ domain › POZ domain › POZ domain › DUF7754 0.68 57.0 3.82e-01 95.2% 24.7%
3489849 5.1.4.74 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Vps16_N 0.68 58.0 3.48e-01 98.4% 18.1%
3681959 109.27.1.3 alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain › NPH3 0.68 58.0 4.38e-01 95.2% 42.0%
4584262 3222.1.1.1 a+b complex topology › Regulatory domain of isocitrate dehydrogenase kinase/phosphatase › Regulatory domain of isocitrate dehydrogenase kinase/phosphatase › Regulatory domain of isocitrate dehydrogenase kinase/phosphatase › AceK_regulatory 0.67 53.0 3.49e-01 92.1% 36.1%
3221809 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.65 50.0 5.13e-01 84.1% 100.0%
4451518 101.1.1.80 alpha arrays › HTH › HTH › Three-helical HTH › PRC2_HTH_1 0.64 43.0 4.22e-01 71.4% 90.0%
4567912 109.4.1.109 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1 0.61 50.0 3.66e-01 93.7% 31.9%
3480326 109.40.1.2 alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.61 53.0 4.29e-01 100.0% 52.0%
3676280 109.4.1.62 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Nic96 0.60 52.0 4.13e-01 98.4% 65.4%
3610895 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 49.0 3.37e-01 98.4% 31.6%
4413999 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.59 47.0 4.62e-01 90.5% 87.1%
4484053 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.59 51.0 4.86e-01 100.0% 89.3%
3596374 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 48.0 2.72e-01 98.4% 15.1%
3934211 3265.1.1.1 alpha arrays › C-terminal helical domain in tRNA modifying enzyme GidA › C-terminal helical domain in tRNA modifying enzyme GidA › C-terminal helical domain in tRNA modifying enzyme GidA › GIDA_C_1st 0.58 41.0 3.76e-01 76.2% 92.9%
4993658 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 45.0 3.75e-01 85.7% 63.7%
4232831 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.57 45.0 4.47e-01 88.9% 92.3%
5000247 184.1.1.0 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N 0.57 39.0 3.86e-01 87.3% 69.2%
3219854 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 48.0 3.28e-01 98.4% 57.6%
4180560 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 47.0 3.42e-01 95.2% 32.1%
5020289 3883.1.1.1 alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.56 49.0 3.45e-01 98.4% 81.9%
3830808 109.4.1.1287 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_6, TPR_8, TPR_16 0.56 46.0 2.91e-01 92.1% 17.7%
4405099 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.55 45.0 4.39e-01 93.7% 91.4%
4355361 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.54 42.0 4.17e-01 92.1% 84.3%
3913629 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.53 42.0 3.98e-01 90.5% 80.0%
3736053 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.53 46.0 4.06e-01 98.4% 81.1%
3957483 243.1.1.77 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF29518 0.53 44.0 3.44e-01 92.1% 87.4%
5051840 601.28.1.0 alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.53 43.0 3.93e-01 90.5% 85.9%
4397003 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.53 36.0 3.80e-01 74.6% 100.0%
4076215 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.52 41.0 4.06e-01 93.7% 91.4%
3967073 601.3.1.0 alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.52 43.0 3.53e-01 92.1% 95.0%
4116499 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.52 42.0 4.17e-01 95.2% 92.9%
4390167 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.52 40.0 4.01e-01 88.9% 90.8%
3803125 633.4.1.1 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.51 38.0 2.86e-01 84.1% 59.2%
3407072 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.51 42.0 3.94e-01 92.1% 85.0%
D2 high residues 92-175
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23817.2 best DUF7188 175.7 1.20e-51 100.0% 44.9%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z05A01 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 0.65 45.0 4.84e-01 97.6% 83.3%
3ljlA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.62 44.0 3.65e-01 75.0% 72.5%
3iuoA00 1.10.10.1390 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › ATP-dependent DNA helicase RecQ 0.60 46.0 4.22e-01 100.0% 63.3%
5zyrA02 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 0.54 39.0 3.22e-01 76.2% 92.1%
3bruB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 41.0 3.23e-01 89.3% 71.4%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 45.0 3.58e-01 100.0% 72.4%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3931341 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.75 54.0 5.29e-01 92.9% 70.0%
5072288 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.68 45.0 4.68e-01 72.6% 72.5%
4948474 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.67 48.0 5.23e-01 91.7% 90.0%
5074940 101.1.6.0 alpha arrays › HTH › HTH › TrpR 0.66 42.0 5.04e-01 92.9% 100.0%
5075830 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 45.0 4.10e-01 86.9% 54.5%
5020571 101.1.1.101 alpha arrays › HTH › HTH › Three-helical HTH › HTH_40 0.65 48.0 4.43e-01 100.0% 61.9%
5010592 101.1.2.68 alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc34 0.65 47.0 4.16e-01 92.9% 53.3%
5045749 101.1.11.203 alpha arrays › HTH › HTH › Ribbon-helix-helix › UPF0175 0.63 45.0 4.94e-01 75.0% 96.9%
4394488 101.35.1.19 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH2+RecX_HTH1 0.51 42.0 4.15e-01 91.7% 95.6%