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NC_041929.1__YP_009601468.1__FDH46_gp135__00343

Bact-Vir

NC_041929.1__YP_009601468.1__FDH46_gp135__00343

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

72.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 4-68
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1y4oA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.68 40.0 3.38e-01 87.7% 36.5%
2uz8A01 3.40.30.90 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.67 43.0 4.66e-01 72.3% 79.6%
2nn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.66 48.0 3.62e-01 80.0% 81.3%
2jvnA00 3.90.640.80 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.60 49.0 3.97e-01 90.8% 46.8%
1tmoA03 3.90.55.10 Alpha Beta › Alpha-Beta Complex › Dimethylsulfoxide Reductase; domain 3 › Dimethylsulfoxide Reductase, domain 3 0.59 33.0 2.99e-01 83.1% 41.9%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 49.0 4.12e-01 92.3% 75.2%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 53.0 4.66e-01 100.0% 79.8%
4an6B00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.57 40.0 3.00e-01 73.8% 69.0%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 48.0 4.06e-01 92.3% 71.7%
5ly3A02 3.30.420.570 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.56 38.0 2.65e-01 70.8% 71.9%
2nysA00 2.30.30.220 Mainly Beta › Roll › SH3 type barrels. › SspB-like 0.56 48.0 3.98e-01 96.9% 88.0%
1loxA01 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.55 49.0 2.98e-01 100.0% 76.0%
6muwB00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.55 43.0 3.08e-01 90.8% 31.0%
2zovA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.54 45.0 3.33e-01 90.8% 74.1%
3fm2A00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.54 37.0 2.99e-01 72.3% 68.4%
4q05A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 41.0 2.71e-01 87.7% 89.0%
6liuC02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 45.0 3.80e-01 100.0% 91.4%
3a0oA03 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 39.0 2.62e-01 83.1% 77.9%
4ok4A02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 35.0 2.28e-01 73.8% 84.5%
1ln1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.50 37.0 2.72e-01 83.1% 68.0%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3702975 3556.1.1.0 ↗ a+b two layers › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 0.75 39.0 3.38e-01 90.8% 35.1%
4927204 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.75 38.0 3.39e-01 93.8% 36.7%
4282578 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.73 50.0 4.74e-01 75.4% 58.7%
5046079 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.69 61.0 3.89e-01 100.0% 70.1%
4618205 604.1.1.150 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF28954 0.67 49.0 4.05e-01 83.1% 42.5%
4944343 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.67 41.0 3.62e-01 93.8% 42.6%
5048580 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.66 37.0 3.38e-01 93.8% 39.3%
3928506 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.65 46.0 4.21e-01 73.8% 65.9%
4008034 223.1.1.113 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30408 0.65 49.0 3.53e-01 84.6% 30.6%
3240894 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.64 51.0 3.37e-01 86.2% 67.5%
3997608 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.63 45.0 3.01e-01 76.9% 61.5%
3356481 386.1.1.117 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7028 0.63 44.0 4.10e-01 73.8% 97.6%
3578637 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.63 45.0 2.98e-01 76.9% 60.3%
5000789 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.63 54.0 4.58e-01 93.8% 67.6%
3939998 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.61 49.0 3.30e-01 87.7% 67.1%
3785619 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.61 52.0 4.30e-01 93.8% 61.7%
4934384 101.1.2.947 ↗ alpha arrays › HTH › HTH › winged helix domain › PF27234 0.61 41.0 3.77e-01 70.8% 78.8%
3804264 64.1.1.8 ↗ beta meanders › WW domain-like › WW domain › WW domain › DUF7028 0.60 42.0 3.94e-01 75.4% 89.4%
5022358 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.60 41.0 3.44e-01 70.8% 81.7%
3470536 239.3.1.0 ↗ beta barrels › Ribosomal protein L25-like › FAS1 domain › FAS1 domain 0.58 40.0 3.30e-01 75.4% 88.9%
3645375 386.1.1.117 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7028 0.58 40.0 3.67e-01 75.4% 84.0%
3682992 601.23.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III 0.58 51.0 3.30e-01 98.5% 25.6%
3522390 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 50.0 3.78e-01 93.8% 94.4%
5061404 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.55 42.0 2.76e-01 84.6% 38.0%
4498285 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.55 44.0 3.87e-01 86.2% 87.4%
3789270 5.1.4.115 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CRT10 0.53 37.0 2.21e-01 72.3% 70.8%
4203006 4.1.1.7 ↗ beta barrels › SH3 › SH3 › SH3 › KOW,ribosomal_L24 0.53 41.0 3.48e-01 84.6% 55.5%
4961948 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.53 39.0 3.23e-01 78.5% 67.5%
5048423 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 39.0 3.23e-01 86.2% 45.2%
5048237 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.51 36.0 2.93e-01 73.8% 98.4%
3615162 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 42.0 2.56e-01 92.3% 38.0%
3659428 3556.1.1.1 ↗ a+b two layers › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 › DUF3223 0.50 34.0 3.06e-01 70.8% 94.8%
2124201 220.3.1.2 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.50 36.0 2.85e-01 80.0% 68.4%