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NC_041929.1__YP_009601167.1__FDH46_gp042__00042

Bact-Vir

NC_041929.1__YP_009601167.1__FDH46_gp042__00042

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

67.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 11-66
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ddvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.78 50.0 4.04e-01 83.9% 35.6%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.76 57.0 5.47e-01 100.0% 69.7%
5d4nC00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 62.0 5.09e-01 100.0% 84.7%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.68 58.0 4.10e-01 100.0% 31.7%
2byeA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.67 53.0 4.47e-01 100.0% 50.5%
5uejA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 59.0 4.67e-01 100.0% 96.5%
3k59A02 3.30.70.2250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › B family DNA polymerase, N domain, alpha/beta motif 0.65 55.0 5.24e-01 94.6% 100.0%
2dt9A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.65 57.0 5.08e-01 98.2% 98.7%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 52.0 4.52e-01 100.0% 57.6%
4u9cA01 2.40.128.250 Mainly Beta › Beta Barrel › Lipocalin › 0.62 52.0 4.14e-01 100.0% 90.3%
1uenA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 52.0 3.99e-01 100.0% 41.6%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 50.0 4.32e-01 100.0% 58.5%
2djwA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.60 49.0 4.63e-01 100.0% 98.6%
2qv6A01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.59 50.0 3.95e-01 100.0% 68.0%
5u8rA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 51.0 4.11e-01 100.0% 50.9%
2outA01 3.40.5.80 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.58 47.0 4.71e-01 98.2% 89.5%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.57 47.0 4.29e-01 100.0% 97.6%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.57 48.0 4.32e-01 100.0% 92.9%
4a18X01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 48.0 4.39e-01 100.0% 74.7%
3s2cJ01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 47.0 3.52e-01 100.0% 37.1%
4lvnP00 3.30.70.2380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 49.0 4.35e-01 100.0% 95.1%
4gucA00 2.60.40.3720 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 48.0 3.86e-01 100.0% 49.6%
3vs8H00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.56 44.0 2.72e-01 89.3% 49.5%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 45.0 3.68e-01 100.0% 47.2%
1y7xA02 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.55 42.0 4.29e-01 100.0% 85.7%
3o1lB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.55 46.0 4.06e-01 100.0% 92.0%
4bz4A00 2.60.120.1220 Mainly Beta › Sandwich › Jelly Rolls › 0.55 42.0 3.00e-01 89.3% 26.6%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.54 44.0 4.06e-01 100.0% 98.7%
3nrbB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 44.0 4.01e-01 100.0% 95.2%
2cuiA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 45.0 3.67e-01 100.0% 49.1%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 43.0 3.91e-01 100.0% 96.4%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.53 37.0 2.97e-01 75.0% 81.0%
4gioA00 2.60.40.3230 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 45.0 3.84e-01 100.0% 58.3%
2llzA01 3.30.70.2360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 42.0 3.76e-01 100.0% 88.9%
4i3gA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.44e-01 96.4% 63.2%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3595127 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.70 64.0 5.95e-01 100.0% 100.0%
3911249 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.68 46.0 3.94e-01 100.0% 42.1%
3397457 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.68 52.0 5.15e-01 100.0% 80.0%
5016503 77.1.1.0 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein 0.66 57.0 4.64e-01 100.0% 56.4%
3250928 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.66 56.0 5.01e-01 96.4% 100.0%
3540023 382.1.1.1 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.64 56.0 4.79e-01 100.0% 66.7%
4642338 807.1.1.1 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.63 51.0 5.27e-01 100.0% 96.2%
3252771 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.63 55.0 4.85e-01 100.0% 67.1%
4929768 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.63 54.0 5.00e-01 100.0% 100.0%
5025566 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.62 55.0 5.63e-01 100.0% 100.0%
5035588 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.61 52.0 4.83e-01 100.0% 96.0%
3511265 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 53.0 4.29e-01 100.0% 50.0%
4929272 304.22.1.0 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain 0.61 53.0 4.74e-01 100.0% 91.3%
3274364 560.1.1.0 ↗ few secondary structure elements › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain 0.61 45.0 4.77e-01 98.2% 95.9%
5011383 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.60 51.0 5.08e-01 100.0% 95.0%
5002742 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.60 53.0 5.34e-01 98.2% 100.0%
3601653 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.60 41.0 3.05e-01 73.2% 59.3%
4007645 304.146.1.0 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein yjdK › Uncharacterized protein yjdK 0.59 52.0 4.45e-01 100.0% 88.9%
5050551 876.1.1.0 ↗ a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.58 50.0 3.70e-01 98.2% 97.3%
411813 3335.1.1.2 ↗ beta barrels › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › TbpB_A 0.58 49.0 3.97e-01 100.0% 74.6%
3223928 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.57 48.0 4.28e-01 100.0% 71.8%
3487137 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 48.0 3.68e-01 100.0% 40.8%
4947071 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.57 49.0 4.40e-01 100.0% 96.2%
3732370 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.57 49.0 4.81e-01 100.0% 91.7%
3219365 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.56 49.0 4.03e-01 100.0% 58.1%
3264859 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 49.0 4.03e-01 100.0% 54.3%
4981984 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 49.0 4.08e-01 100.0% 58.0%
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.56 44.0 4.64e-01 100.0% 100.0%
None — 0.56 46.0 2.95e-01 100.0% 19.1%
3623001 284.2.1.0 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.55 45.0 4.12e-01 98.2% 98.8%
3687649 10.12.1.101 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC, Cupin_8 0.55 46.0 2.94e-01 100.0% 24.1%
3988500 4342.1.1.1 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › Tex_central_region 0.55 40.0 2.94e-01 85.7% 76.8%
3180683 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 44.0 3.60e-01 100.0% 47.3%
3312666 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 41.0 3.88e-01 100.0% 70.0%
4585893 1.1.2.22 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › IML1_N_fung 0.54 47.0 3.85e-01 100.0% 67.6%
5070107 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.53 44.0 4.20e-01 100.0% 100.0%
3892842 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.53 42.0 4.13e-01 100.0% 83.1%
3517068 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.53 43.0 4.18e-01 100.0% 87.7%
3565284 223.2.1.21 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › AP-5_subunit_s1 0.52 40.0 2.85e-01 87.5% 32.0%
5039035 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.52 45.0 3.82e-01 100.0% 83.7%
4121956 11.1.1.1280 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF29750 0.52 44.0 3.57e-01 100.0% 48.7%
4031329 4342.1.1.1 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › Tex_central_region 0.52 40.0 2.88e-01 92.9% 78.6%
3851316 223.2.1.19 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_1 0.52 39.0 2.88e-01 85.7% 68.2%
3994441 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.51 41.0 3.33e-01 100.0% 44.2%
4928213 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.50 42.0 4.02e-01 100.0% 100.0%
3593924 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.50 42.0 3.42e-01 100.0% 50.8%