←Back to structures

NC_041911.1__YP_009598843.1__FDH28_gp271__00150

Bact-Vir

NC_041911.1__YP_009598843.1__FDH28_gp271__00150

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

90.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (8 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 3-52
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3mazA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.68 59.0 4.72e-01 98.0% 66.7%
7pi0S01 1.10.3460.10 Mainly Alpha › Orthogonal Bundle › Chlorophyll a-b binding protein › Chlorophyll a/b binding protein domain 0.68 47.0 3.19e-01 74.0% 77.1%
4i8oA04 6.10.250.2650 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.66 44.0 3.48e-01 80.0% 34.7%
2wmmA02 3.30.70.3500 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › MukB, hinge domain 0.65 40.0 3.07e-01 82.0% 26.5%
3d1cA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.65 40.0 3.09e-01 94.0% 26.3%
2nnwA01 3.30.420.220 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.65 54.0 4.15e-01 98.0% 45.1%
2codA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 47.0 3.90e-01 94.0% 42.7%
3d6wB02 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.63 43.0 4.67e-01 88.0% 92.3%
4k22B01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 44.0 2.83e-01 74.0% 45.3%
4bjzA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 44.0 3.05e-01 74.0% 60.7%
3hr8A02 3.30.250.10 Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › RecA protein, C-terminal domain 0.63 43.0 3.90e-01 98.0% 49.3%
2ch5B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 51.0 3.44e-01 94.0% 67.5%
4phtY02 3.30.420.370 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › GspL cytoplasmic domain, C-terminal subdomain 0.58 46.0 4.36e-01 90.0% 77.4%
4p79A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.58 45.0 3.17e-01 90.0% 69.1%
1upqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 46.0 3.72e-01 94.0% 45.8%
2olsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.57 42.0 3.04e-01 78.0% 72.7%
1vw4F02 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.57 48.0 4.04e-01 100.0% 66.3%
3ligA02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.57 45.0 3.17e-01 100.0% 26.0%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 48.0 3.98e-01 94.0% 63.2%
3rp7A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 45.0 3.16e-01 90.0% 91.1%
4o2zA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.56 48.0 3.48e-01 100.0% 81.0%
1y13A00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.56 48.0 3.45e-01 100.0% 76.7%
2xdoD00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 47.0 2.77e-01 92.0% 94.8%
5cflA02 3.40.50.12100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Stimulator of interferon genes protein 0.55 47.0 3.43e-01 100.0% 67.3%
4dzoA02 3.30.457.60 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.55 48.0 4.18e-01 100.0% 75.3%
2dn6A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 43.0 3.48e-01 100.0% 41.7%
7o06C01 3.30.1470.10 Alpha Beta › 2-Layer Sandwich › Photosystem 1 Reaction Centre Subunit Ii; Chain: D; › Photosystem I PsaD, reaction center subunit II 0.54 45.0 3.71e-01 94.0% 78.0%
4nswA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.32e-01 100.0% 40.4%
3pnnA00 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 0.53 39.0 2.54e-01 88.0% 90.4%
4pdyA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 39.0 3.16e-01 82.0% 70.7%
4z3xA03 1.10.569.10 Mainly Alpha › Orthogonal Bundle › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 0.52 45.0 3.10e-01 100.0% 54.8%
5e75A00 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.52 44.0 2.56e-01 98.0% 9.5%
2ymsA00 2.40.128.630 Mainly Beta › Beta Barrel › Lipocalin › 0.52 42.0 3.30e-01 98.0% 49.2%
1mtpA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.52 46.0 3.73e-01 98.0% 62.6%
5y6qB02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.51 41.0 3.43e-01 100.0% 57.5%
2esvD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 42.0 3.44e-01 100.0% 81.7%
2q0lA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 45.0 3.06e-01 100.0% 96.3%
3ng7X01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 43.0 2.90e-01 100.0% 36.2%
3qj4A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 40.0 2.85e-01 90.0% 44.0%
3ol0B00 6.20.90.30 Special › Other non-globular › SH3 type barrels. › 0.50 31.0 3.26e-01 88.0% 70.7%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.50 44.0 3.55e-01 100.0% 85.9%
1es6A02 2.60.510.10 Mainly Beta › Sandwich › EV matrix protein fold › EV matrix protein 0.50 40.0 3.41e-01 100.0% 51.5%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4862553 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.75 45.0 3.53e-01 96.0% 30.0%
4208229 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.69 44.0 4.50e-01 94.0% 66.0%
3168947 874.1.1.0 ↗ a+b duplicates or obligate multimers › Smc hinge domain › Smc hinge domain › Smc hinge domain 0.67 41.0 2.75e-01 74.0% 15.9%
3640588 6043.2.1.0 ↗ a+b two layers › yfeY-like › Teichoic acid transporter subunit TagH C-terminal domain › Teichoic acid transporter subunit TagH C-terminal domain 0.67 48.0 3.78e-01 76.0% 99.1%
4998118 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.66 48.0 4.39e-01 90.0% 60.0%
5032493 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.66 48.0 4.55e-01 90.0% 66.1%
4982571 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.65 46.0 4.41e-01 90.0% 65.5%
3535695 1021.1.1.2 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › RNA_hel_CTD 0.65 43.0 3.51e-01 100.0% 35.8%
3403184 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.64 54.0 4.40e-01 98.0% 84.0%
4683204 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.64 46.0 3.67e-01 100.0% 37.1%
3471371 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 46.0 3.51e-01 96.0% 35.5%
4484289 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.62 40.0 2.72e-01 90.0% 17.4%
3381251 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 45.0 3.84e-01 78.0% 67.5%
4014861 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.61 44.0 2.89e-01 100.0% 16.7%
4939428 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.60 44.0 4.20e-01 84.0% 66.7%
4599953 3292.1.1.0 ↗ a+b complex topology › Adenine deaminase 2 C-terminal domain › Adenine deaminase 2 C-terminal domain › Adenine deaminase 2 C-terminal domain 0.60 51.0 3.45e-01 100.0% 55.2%
4664955 318.1.1.0 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 0.60 52.0 4.31e-01 100.0% 67.8%
4200480 318.1.1.1 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal_L6 0.58 51.0 4.10e-01 100.0% 61.0%
4255188 318.1.1.0 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 0.58 50.0 4.18e-01 100.0% 66.7%
3731822 5.1.4.169 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RSE1_2nd 0.57 49.0 2.93e-01 98.0% 21.0%
4983508 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 50.0 4.49e-01 98.0% 97.1%
3279244 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 50.0 4.03e-01 100.0% 85.0%
3659226 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.57 46.0 3.04e-01 92.0% 100.0%
5076406 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 48.0 4.01e-01 94.0% 81.2%
3236918 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.57 44.0 3.71e-01 100.0% 48.9%
3721597 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.56 47.0 2.92e-01 94.0% 24.2%
4968450 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 44.0 4.30e-01 90.0% 81.8%
4473548 304.51.1.2 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › RAMPs 0.55 41.0 2.60e-01 84.0% 82.0%
5051602 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.54 43.0 2.68e-01 100.0% 17.5%
4037872 2003.1.3.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.54 43.0 2.71e-01 88.0% 36.1%
5035361 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.53 42.0 3.67e-01 100.0% 55.6%
3372534 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.52 43.0 3.14e-01 96.0% 61.9%
4511789 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.52 44.0 2.56e-01 94.0% 40.5%
5074340 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.52 46.0 3.33e-01 100.0% 84.3%
4986756 206.1.3.9 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Synapsin_C 0.52 42.0 2.62e-01 88.0% 20.7%
4792845 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 43.0 2.98e-01 100.0% 56.9%
5011765 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.52 45.0 3.32e-01 100.0% 84.4%
3794367 5.1.3.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Arylesterase 0.52 42.0 2.88e-01 100.0% 41.3%
5033675 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.51 44.0 2.69e-01 100.0% 40.3%
4942997 2005.1.1.7 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.51 42.0 2.69e-01 96.0% 29.1%
3838855 2003.1.3.8 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › Mqo 0.51 40.0 2.46e-01 100.0% 95.7%
2879522 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.50 38.0 3.27e-01 88.0% 80.4%
D2 high residues 58-136
PDB
Domain cluster: rep: JSantini_GMIN_scaffold_8_prodigal-single.1__X__X__00552__D59-137