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NC_070857.1__YP_010658417.1__PP751_gp013__00013

Bact-Vir

NC_070857.1__YP_010658417.1__PP751_gp013__00013

Identity

Accession:
NC_070857 ↗
Kingdom:
phage

Quality

89.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Xoxocotlavirus› Rhizobium_phage_RHph_X2_28B

TaxID: 2836086

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 16-68
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.71 39.0 4.25e-01 100.0% 64.4%
3mogC02 1.10.1040.50 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › 0.70 55.0 3.82e-01 90.6% 29.5%
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.69 40.0 3.10e-01 98.1% 27.0%
5f64A02 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 0.68 50.0 4.58e-01 86.8% 58.7%
6hxlB01 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.67 56.0 4.26e-01 92.5% 81.0%
2l09A01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.66 37.0 3.77e-01 100.0% 55.8%
3b0bB00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.64 44.0 3.55e-01 96.2% 39.2%
1x4oA00 1.10.10.790 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module 0.61 44.0 3.98e-01 79.2% 62.8%
2oceA01 1.10.10.650 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › RuvA domain 2-like 0.61 49.0 4.04e-01 100.0% 65.5%
7s03A01 1.10.10.1450 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.61 45.0 4.64e-01 83.0% 100.0%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.61 46.0 4.23e-01 90.6% 64.1%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 48.0 4.32e-01 100.0% 64.1%
3na7A00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 48.0 3.15e-01 100.0% 21.5%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.56 49.0 4.24e-01 100.0% 64.7%
1b04A03 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.55 42.0 4.09e-01 96.2% 74.2%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 46.0 4.40e-01 94.3% 87.1%
8f76A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.55 49.0 3.09e-01 100.0% 20.0%
3jtgA01 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 0.55 41.0 3.71e-01 90.6% 80.0%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 49.0 3.61e-01 100.0% 39.1%
5k3hB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.54 49.0 3.61e-01 100.0% 40.6%
1hbkA00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.53 44.0 3.76e-01 94.3% 64.0%
1pn9B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 42.0 3.21e-01 100.0% 36.2%
2janA02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.52 36.0 3.15e-01 79.2% 76.2%
2rvqC01 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.51 37.0 3.37e-01 81.1% 56.6%
2be4A02 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 37.0 3.05e-01 79.2% 94.1%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046154 129.1.1.2 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 3HCDH 0.70 56.0 4.96e-01 90.6% 70.9%
4928812 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.68 54.0 4.60e-01 92.5% 58.9%
3724068 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 49.0 4.92e-01 79.2% 81.8%
3988910 101.1.1.382 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DDE_Tnp_IS66 0.67 51.0 5.42e-01 86.8% 100.0%
3910504 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 51.0 5.28e-01 84.9% 90.0%
4969058 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.67 52.0 4.60e-01 90.6% 65.9%
3506989 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.67 48.0 4.95e-01 77.4% 86.0%
5040582 129.1.1.2 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 3HCDH 0.66 52.0 4.65e-01 90.6% 70.0%
3544446 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.66 49.0 4.72e-01 79.2% 70.0%
3901968 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 46.0 5.06e-01 77.4% 100.0%
4034503 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.66 51.0 4.78e-01 94.3% 69.2%
3715279 101.1.1.276 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding, Myb_DNA-bind_6 0.66 54.0 3.86e-01 98.1% 32.2%
3937317 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.65 47.0 4.85e-01 79.2% 88.0%
2393452 101.43.1.1 ↗ alpha arrays › HTH › Phage G20C small terminase N-terminal domain › Phage G20C small terminase N-terminal domain › TerS_N 0.65 52.0 5.13e-01 92.5% 92.9%
4945040 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.65 49.0 4.73e-01 83.0% 73.3%
3931083 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.65 46.0 4.73e-01 77.4% 86.0%
3629477 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.65 53.0 5.23e-01 100.0% 98.3%
3941666 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.65 51.0 4.67e-01 90.6% 67.6%
3522325 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.65 50.0 4.77e-01 88.7% 86.2%
4979742 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.65 49.0 4.34e-01 84.9% 61.3%
4959187 101.1.2.489 ↗ alpha arrays › HTH › HTH › winged helix domain › Transposase_mut 0.64 48.0 4.96e-01 86.8% 92.0%
3960420 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.64 51.0 3.97e-01 96.2% 38.4%
5029224 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 53.0 5.17e-01 100.0% 90.0%
2627770 101.1.4.1 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › Pou 0.63 45.0 4.15e-01 75.5% 63.2%
4501343 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.63 45.0 4.47e-01 77.4% 80.0%
3980764 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 46.0 4.79e-01 84.9% 97.8%
5016992 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 44.0 4.68e-01 75.5% 91.1%
3928087 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.63 49.0 4.57e-01 88.7% 80.0%
3590474 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 50.0 4.37e-01 92.5% 60.0%
3740014 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 48.0 4.46e-01 90.6% 67.1%
5047162 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 44.0 4.21e-01 79.2% 66.2%
3475184 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.61 47.0 4.55e-01 84.9% 75.0%
4473504 304.136.1.3 ↗ a+b two layers › Alpha-beta plaits › Oligo-peptide binding protein (OPPA) insertion domain › Oligo-peptide binding protein (OPPA) insertion domain › SGIII 0.61 44.0 3.78e-01 79.2% 56.7%
3793542 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.61 49.0 4.81e-01 98.1% 95.0%
4990274 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.61 50.0 4.18e-01 100.0% 80.0%
3987909 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 0.61 50.0 3.85e-01 98.1% 63.7%
4958195 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.61 47.0 4.75e-01 98.1% 92.7%
3617137 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 45.0 4.52e-01 86.8% 96.4%
5079851 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 49.0 4.79e-01 100.0% 90.0%
3358320 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.60 45.0 4.56e-01 86.8% 92.7%
4014657 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 44.0 4.41e-01 84.9% 85.5%
4926838 101.43.1.0 ↗ alpha arrays › HTH › Phage G20C small terminase N-terminal domain › Phage G20C small terminase N-terminal domain 0.60 47.0 4.53e-01 92.5% 78.5%
3184342 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 46.0 4.54e-01 90.6% 85.0%
4274627 101.1.1.266 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Transposase_mut 0.60 45.0 4.40e-01 98.1% 76.7%
4008061 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 43.0 3.90e-01 79.2% 64.0%
5079733 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 44.0 4.07e-01 84.9% 64.0%
3966077 101.26.1.1 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › Tex_N 0.59 44.0 4.19e-01 88.7% 95.7%
4984058 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.59 40.0 4.27e-01 73.6% 97.8%
4615565 101.1.1.249 ↗ alpha arrays › HTH › HTH › Three-helical HTH › SGIII 0.58 41.0 3.63e-01 77.4% 58.8%
3291561 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.58 46.0 4.19e-01 100.0% 64.0%
3962579 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 46.0 3.62e-01 100.0% 92.1%
3365315 101.1.1.291 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PF26175 0.57 40.0 4.02e-01 79.2% 85.5%
3589089 101.1.2.489 ↗ alpha arrays › HTH › HTH › winged helix domain › Transposase_mut 0.56 42.0 3.55e-01 90.6% 44.8%
3610601 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.56 51.0 3.33e-01 100.0% 25.8%
3716198 4992.1.1.0 ↗ extended segments › RelB-like › RelB-like › RelB-like 0.56 49.0 3.79e-01 100.0% 45.8%
4959424 103.6.1.0 ↗ alpha arrays › RuvA-C › FGAM synthase PurL, linker domain › FGAM synthase PurL, linker domain 0.56 43.0 4.26e-01 90.6% 98.2%
3574709 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 39.0 3.84e-01 79.2% 80.0%
3575777 101.43.1.0 ↗ alpha arrays › HTH › Phage G20C small terminase N-terminal domain › Phage G20C small terminase N-terminal domain 0.55 39.0 4.03e-01 84.9% 96.0%
3618803 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.54 41.0 4.05e-01 90.6% 90.0%
3980428 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 0.54 49.0 4.33e-01 100.0% 73.3%
3690648 109.1.1.35 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › PF25907 0.54 41.0 3.14e-01 92.5% 64.4%
4031838 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.54 40.0 3.68e-01 90.6% 86.3%
4474912 377.4.1.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › YlxR-like › YlxR-like › YlxR 0.52 42.0 3.68e-01 98.1% 78.9%