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NC_041911.1__YP_009598763.1__FDH28_gp070__00070

Bact-Vir

NC_041911.1__YP_009598763.1__FDH28_gp070__00070

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

83.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (47 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 13-79
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1g0sA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.66 45.0 3.20e-01 76.1% 23.4%
6gmhH01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 36.0 2.86e-01 76.1% 26.4%
5ih0A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 42.0 3.83e-01 100.0% 53.8%
2xzmP00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 35.0 2.84e-01 77.6% 29.7%
3hhjB00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.54 42.0 3.43e-01 86.6% 62.6%
2arhA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 38.0 2.93e-01 97.0% 31.6%
2xglA00 3.10.450.300 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › YebF/Colicin-M immunity protein 0.53 45.0 4.17e-01 100.0% 80.2%
3mcrA00 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.52 42.0 3.31e-01 91.0% 41.6%
4b63A00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 46.0 2.81e-01 100.0% 34.8%
4xhvA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.52 38.0 3.51e-01 82.1% 71.3%
3sxxD02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 44.0 3.83e-01 100.0% 69.7%
3nv0B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 42.0 3.55e-01 100.0% 77.2%
1s0wC01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.51 38.0 3.48e-01 80.6% 67.0%
6fgjA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.51 42.0 3.28e-01 91.0% 82.0%
2fmlA02 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.51 40.0 3.19e-01 92.5% 67.7%
1u7iA01 3.30.720.100 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.50 36.0 3.62e-01 91.0% 77.3%
2be3B01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.50 42.0 3.46e-01 98.5% 83.0%
5amhA00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.50 43.0 3.74e-01 98.5% 93.4%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3225640 220.1.1.168 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Tmpp129 0.61 49.0 4.06e-01 91.0% 62.4%
3817109 243.3.1.26 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › protein_MS5 0.59 51.0 3.99e-01 100.0% 48.4%
3393710 304.9.1.95 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF4780 0.58 46.0 4.14e-01 88.1% 82.1%
3721396 243.5.1.0 ↗ a+b two layers › Cystatin-like › Amine oxidase N-terminal region › Amine oxidase N-terminal region 0.56 48.0 4.37e-01 100.0% 73.7%
3941717 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.56 48.0 4.47e-01 100.0% 79.5%
3699926 304.51.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.56 45.0 3.69e-01 91.0% 70.0%
3627521 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.56 44.0 3.87e-01 97.0% 58.0%
3233399 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.55 41.0 3.75e-01 95.5% 57.9%
3498599 2.3.1.1 ↗ beta barrels › OB-fold › TIMP-like › TIMP-like › TIMP 0.55 46.0 3.40e-01 95.5% 38.0%
3398510 206.1.1.55 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › EcKL 0.55 47.0 2.93e-01 100.0% 28.4%
3281968 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 40.0 3.69e-01 83.6% 61.1%
3212183 922.1.1.0 ↗ few secondary structure elements › TSP-1 type 1 repeat › TSP-1 type 1 repeat › TSP-1 type 1 repeat 0.53 33.0 3.78e-01 71.6% 93.3%
None — 0.53 47.0 2.84e-01 100.0% 34.0%
3613691 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.53 41.0 3.54e-01 89.6% 78.3%
1688895 2003.1.3.4 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › Lys_Orn_oxgnase 0.53 46.0 3.40e-01 100.0% 83.5%
3589805 243.8.1.0 ↗ a+b two layers › Cystatin-like › Uracil-DNA glycosylase inhibitor protein › Uracil-DNA glycosylase inhibitor protein 0.53 46.0 4.13e-01 100.0% 97.9%
3572958 389.1.2.1 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.53 36.0 3.80e-01 94.0% 80.0%
3390019 304.151.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase 0.53 41.0 3.57e-01 88.1% 80.0%
3246008 922.1.1.0 ↗ few secondary structure elements › TSP-1 type 1 repeat › TSP-1 type 1 repeat › TSP-1 type 1 repeat 0.52 36.0 3.91e-01 73.1% 92.5%
3287954 10.12.1.75 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding_2 0.52 39.0 2.91e-01 88.1% 64.3%
3886741 221.4.1.9 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX_4 0.51 41.0 3.23e-01 91.0% 56.7%
3717718 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 40.0 2.57e-01 88.1% 47.2%
3611783 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.51 39.0 2.91e-01 86.6% 50.0%
3595259 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 41.0 3.33e-01 89.6% 80.8%
3924518 221.4.1.0 ↗ a+b two layers › beta-Grasp › Nudix › Nudix 0.51 38.0 3.30e-01 82.1% 85.5%
3287331 298.1.1.24 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › GFO_IDH_MocA_C3 0.50 39.0 3.08e-01 89.6% 72.5%
3662984 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 35.0 3.35e-01 79.1% 60.0%
D2 high residues 81-155
PDB
Domain cluster: rep: NC_028899.1__YP_009207974.1__AVU11_gp170__00176__D88-154