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NC_041929.1__YP_009601383.1__FDH46_gp220__00258

Bact-Vir

NC_041929.1__YP_009601383.1__FDH46_gp220__00258

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

79.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

Cluster

View cluster (2 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 4-44
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8hi4A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.67 53.0 3.35e-01 97.6% 42.5%
3cgxA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.59 47.0 2.98e-01 95.1% 23.9%
4uc0A00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.56 46.0 2.89e-01 95.1% 22.3%
1qe0A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.55 46.0 2.83e-01 100.0% 33.8%
1tuoA02 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.55 38.0 2.99e-01 92.7% 35.3%
1bxiA00 1.10.1200.20 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Colicin E immunity protein 0.55 43.0 3.55e-01 95.1% 96.4%
1iv0A00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.54 42.0 3.38e-01 97.6% 90.8%
2xryA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 43.0 2.98e-01 95.1% 48.0%
1wznA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 36.0 2.37e-01 70.7% 20.7%
7vi8A01 3.20.20.370 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase/deacetylase 0.53 43.0 2.75e-01 97.6% 98.0%
1y8cA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 39.0 2.61e-01 80.5% 58.6%
3zdbA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.53 43.0 2.96e-01 97.6% 56.7%
5z0qA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.53 43.0 2.76e-01 97.6% 39.2%
2px7A00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.52 43.0 2.83e-01 100.0% 38.9%
2hvwA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.52 43.0 3.00e-01 97.6% 34.0%
6mjgA01 3.40.1010.10 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › Tetrapyrrole methylase, N-terminal domain 0.51 40.0 3.08e-01 100.0% 95.0%
3e38B01 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.50 44.0 2.72e-01 100.0% 35.5%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3270402 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.59 44.0 2.91e-01 82.9% 30.8%
3934189 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.58 49.0 3.07e-01 95.1% 38.6%
3501950 2002.1.1.13 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Aldo_ket_red 0.57 48.0 2.92e-01 97.6% 20.0%
3932223 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.56 47.0 2.93e-01 95.1% 40.0%
3269563 102.1.3.6 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › Nrap_D2 0.56 42.0 2.91e-01 82.9% 82.7%
3428182 210.1.6.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Gamma-glutamyltranspeptidase-like › G_glu_transpept 0.56 44.0 2.87e-01 95.1% 20.5%
4150748 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 47.0 3.15e-01 97.6% 50.6%
3960168 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.55 46.0 4.40e-01 100.0% 88.0%
4097908 4013.1.1.1 ↗ a/b three-layered sandwiches › a/b domain in QueA-like proteins (Pfam 02547) › a/b domain in QueA-like proteins (Pfam 02547) › a/b domain in QueA-like proteins (Pfam 02547) › Queuosine_synth 0.54 45.0 2.86e-01 100.0% 38.3%
4132227 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.52 43.0 2.60e-01 97.6% 17.0%
3923014 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.51 39.0 2.68e-01 97.6% 68.0%
3711667 2005.1.1.9 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › DNA_photolyase 0.51 40.0 2.76e-01 97.6% 46.4%
4073869 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.50 40.0 3.53e-01 100.0% 77.1%
4024691 2008.1.1.86 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.50 40.0 3.18e-01 100.0% 51.0%