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NC_041908.1__YP_009598494.1__FDH25_gp52__00052

Bact-Vir

NC_041908.1__YP_009598494.1__FDH25_gp52__00052

Identity

Accession:
NC_041908 ↗
Kingdom:
phage

Quality

85.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Kleczkowskavirus› Rhizobium_phage_RHEph04

TaxID: 1220604

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 8-68
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 59.0 5.89e-01 78.7% 72.6%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 56.0 4.74e-01 77.0% 44.9%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.81 60.0 5.68e-01 100.0% 67.1%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.78 56.0 6.29e-01 100.0% 95.8%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.77 56.0 5.31e-01 78.7% 64.8%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.77 54.0 5.06e-01 78.7% 60.0%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 56.0 5.81e-01 80.3% 82.8%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.75 51.0 4.89e-01 78.7% 62.0%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.74 52.0 5.10e-01 78.7% 68.2%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 54.0 4.42e-01 77.0% 71.4%
6z01B03 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.74 55.0 3.99e-01 78.7% 31.2%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 55.0 5.66e-01 78.7% 84.5%
2qtfA02 6.10.250.2860 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.73 54.0 6.12e-01 98.4% 100.0%
4hb1A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.73 50.0 5.86e-01 72.1% 100.0%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 54.0 5.45e-01 78.7% 93.3%
4akgA02 1.20.140.100 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Dynein motor heavy chain, linker domain, N-terminal subdomain 0.72 54.0 3.82e-01 78.7% 28.6%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.71 52.0 5.29e-01 78.7% 80.3%
1pd3A00 1.10.287.230 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 52.0 5.55e-01 78.7% 94.4%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.70 52.0 4.63e-01 78.7% 61.2%
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 0.70 49.0 5.64e-01 73.8% 100.0%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.70 52.0 5.93e-01 95.1% 100.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.67 48.0 4.79e-01 75.4% 100.0%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.64 47.0 4.70e-01 77.0% 75.8%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 48.0 4.63e-01 80.3% 72.1%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.63 45.0 4.89e-01 80.3% 97.9%
5mmjb02 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.63 45.0 4.81e-01 75.4% 86.5%
3bxjA02 1.10.506.20 Mainly Alpha › Orthogonal Bundle › GTPase Activation - p120GAP; domain 1 › 0.62 50.0 4.31e-01 93.4% 56.1%
7dukB01 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 43.0 4.90e-01 96.7% 97.8%
1twcA01 4.10.860.120 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › RNA polymerase II, clamp domain 0.61 50.0 3.80e-01 86.9% 81.8%
1m56C01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 45.0 4.33e-01 80.3% 72.5%
1cpyA02 1.10.287.410 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 52.0 4.95e-01 96.7% 91.7%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 43.0 3.60e-01 77.0% 43.9%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.60 47.0 4.51e-01 95.1% 73.7%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 43.0 3.63e-01 78.7% 42.9%
1ji0A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 49.0 3.26e-01 91.8% 23.8%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.58 48.0 4.40e-01 93.4% 70.4%
4arvA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.54 39.0 3.20e-01 80.3% 43.7%
2z3xA00 6.10.10.80 Special › Helix non-globular › Helicase, Ruva Protein; domain 3 › Small, acid-soluble spore protein, alpha/beta type-like 0.53 39.0 4.09e-01 91.8% 87.5%
1v4gA01 6.10.140.800 Special › Helix non-globular › Helix Hairpins › 0.53 35.0 3.42e-01 72.1% 60.9%
2xadA00 3.40.50.10320 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › LmbE-like 0.51 43.0 2.84e-01 93.4% 39.0%
4mk3A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 43.0 3.58e-01 100.0% 53.9%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.50 43.0 3.57e-01 100.0% 54.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3609224 3602.1.1.3 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Enkurin 0.88 57.0 5.13e-01 78.7% 51.2%
3569799 605.1.1.136 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Enkurin 0.86 56.0 5.04e-01 78.7% 51.2%
3897805 7022.1.1.1 ↗ alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › MBOAT 0.80 52.0 3.71e-01 78.7% 24.1%
3779372 220.1.1.115 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_19 0.75 56.0 3.88e-01 78.7% 28.9%
5002349 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 0.74 56.0 5.47e-01 78.7% 73.8%
3969942 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.74 53.0 4.21e-01 80.3% 40.0%
3454123 3493.1.1.0 ↗ extended segments › Photosystem II PsbX protein › Photosystem II PsbX protein › Photosystem II PsbX protein 0.72 51.0 5.02e-01 73.8% 69.2%
3318561 616.1.1.2 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › WHEP-TRS 0.72 54.0 5.65e-01 78.7% 94.5%
2546344 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.72 54.0 5.53e-01 80.3% 88.3%
4954852 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.72 53.0 3.69e-01 77.0% 27.2%
3619435 192.8.1.36 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › M_domain 0.69 63.0 5.37e-01 100.0% 88.4%
5002882 4207.1.1.133 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › BREX_BrxC_4th 0.66 59.0 4.61e-01 98.4% 90.4%
4815139 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.65 57.0 4.54e-01 95.1% 75.7%
2834659 5039.1.1.13 ↗ alpha bundles › Cytochrome c oxidase subunit III-like › Cytochrome c oxidase subunit III-like › Cytochrome c oxidase subunit III-like › COX1 0.65 48.0 3.17e-01 80.3% 19.3%
4959130 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.63 45.0 4.34e-01 78.7% 67.1%
3580795 140.1.1.0 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.62 44.0 3.33e-01 77.0% 65.6%
3669948 109.4.1.1495 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF26522 0.61 42.0 2.43e-01 75.4% 6.8%
3713079 5046.1.1.0 ↗ extended segments › F-type ATP synthase subunit b › F-type ATP synthase subunit b › F-type ATP synthase subunit b 0.61 55.0 4.14e-01 96.7% 51.1%
4238998 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 0.61 45.0 4.34e-01 80.3% 88.6%
3841428 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.60 42.0 3.79e-01 78.7% 50.0%
148583 109.1.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C 0.60 42.0 3.48e-01 77.0% 39.2%
3605785 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 50.0 3.30e-01 91.8% 30.8%
3740673 11.2.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PI3K_C2 0.57 45.0 3.16e-01 90.2% 30.0%
3936662 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.57 45.0 2.83e-01 88.5% 16.1%
4023558 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.56 48.0 2.99e-01 95.1% 81.7%
3973702 109.1.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C 0.53 44.0 3.13e-01 96.7% 96.1%
3293917 616.1.1.28 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › RNA_pol_Rpb1_1 0.52 40.0 3.27e-01 85.2% 57.5%