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MN504636.1__QFR59615.1__QuinobequinP09_62__00014

Bact-Vir

MN504636.1__QFR59615.1__QuinobequinP09_62__00014

Identity

Accession:
MN504636 ↗
Kingdom:
phage

Quality

92.4 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 2-57
PDB
Domain cluster: representative
D2 high residues 93-112_139-287
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF18906.6 best Phage_tube_2 48.3 1.40e-12 87.6% 58.3%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4w64B00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.67 54.0 5.54e-01 82.8% 87.5%
4divV01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.67 50.0 5.46e-01 79.3% 94.9%
2q9kA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.64 45.0 4.76e-01 99.4% 81.0%
2qeaB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 44.0 4.61e-01 97.0% 95.5%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4954552 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.86 69.0 7.09e-01 82.2% 98.8%
5078836 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.84 54.0 6.76e-01 81.1% 100.0%
3964955 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.81 64.0 6.64e-01 81.7% 100.0%
4514734 1.1.13.42 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Tail_tube 0.80 52.0 6.33e-01 81.1% 100.0%
4873215 1.1.13.11 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF2001 0.79 61.0 6.66e-01 84.6% 95.7%
4929634 1.1.5.47 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Phage_tube_2 0.79 71.0 5.94e-01 94.1% 62.2%
3502370 1.1.5.47 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Phage_tube_2 0.78 64.0 6.56e-01 84.6% 95.6%
2101633 1.1.13.1 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tube 0.77 60.0 6.08e-01 84.6% 80.8%
3058416 1.1.5.39 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › TssD 0.77 53.0 6.05e-01 82.2% 92.9%
4957560 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.76 57.0 6.46e-01 89.9% 100.0%
3976188 1.1.13.1 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tube 0.76 60.0 6.14e-01 89.3% 83.6%
4157825 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.76 57.0 6.43e-01 86.4% 100.0%
4034209 1.1.13.4 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Sipho_tail 0.72 51.0 5.66e-01 71.6% 100.0%
2387782 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.71 58.0 5.88e-01 85.2% 92.9%
3943316 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.70 63.0 6.53e-01 98.8% 100.0%
3977123 1.1.5.23 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › T6SS_HCP 0.69 56.0 5.79e-01 87.0% 90.0%
3969384 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.68 57.0 5.83e-01 86.4% 92.5%
3265120 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.68 56.0 5.57e-01 85.8% 88.6%
5040464 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.68 35.0 4.58e-01 71.0% 88.4%
4033579 1.1.13.4 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Sipho_tail 0.68 49.0 5.59e-01 74.6% 100.0%
3264744 1.1.5.23 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › T6SS_HCP 0.67 55.0 5.49e-01 85.8% 88.6%
4982153 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.67 53.0 4.51e-01 82.8% 51.9%
1444177 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.67 49.0 5.44e-01 78.1% 94.1%
3059162 1.1.13.30 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › E217_GP41 0.66 47.0 5.45e-01 76.9% 99.2%
4888732 1.1.13.4 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Sipho_tail 0.65 48.0 5.00e-01 78.7% 83.3%
4026305 1.1.5.36 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyrid_ox_like 0.52 47.0 4.54e-01 98.2% 85.8%
D3 medium residues 62-92_113-138
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1jlcB03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 49.0 3.68e-01 75.4% 33.8%
3cygA01 3.30.565.40 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Fervidobacterium nodosum Rt17-B1 like 0.65 46.0 3.67e-01 75.4% 44.5%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.63 43.0 4.09e-01 73.7% 63.4%
1fx3B00 3.10.420.10 Alpha Beta › Roll › Bacterial Protein-export protein SecB › SecB-like 0.63 52.0 3.95e-01 96.5% 75.2%
5cqfA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.62 50.0 3.00e-01 89.5% 28.2%
5n1tA03 3.90.760.10 Alpha Beta › Alpha-Beta Complex › Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 › Flavocytochrome c sulphide dehydrogenase, flavin-binding domain 0.62 48.0 4.57e-01 89.5% 98.6%
2nugB02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.62 42.0 3.96e-01 75.4% 57.7%
1hczA02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.61 43.0 4.29e-01 75.4% 69.5%
3vrdB03 3.90.760.10 Alpha Beta › Alpha-Beta Complex › Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 › Flavocytochrome c sulphide dehydrogenase, flavin-binding domain 0.61 47.0 4.46e-01 89.5% 98.6%
4id2A00 2.40.128.510 Mainly Beta › Beta Barrel › Lipocalin › Protein of unknown function DUF4738 0.61 44.0 3.41e-01 77.2% 92.6%
6gmhC01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.60 45.0 3.45e-01 78.9% 84.9%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 43.0 3.80e-01 78.9% 50.6%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.60 48.0 3.65e-01 89.5% 45.1%
3u1wA01 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 39.0 2.75e-01 75.4% 21.3%
2lccA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 40.0 3.74e-01 77.2% 53.9%
2f8xC01 2.60.40.1450 Mainly Beta › Sandwich › Immunoglobulin-like › LAG1, DNA binding domain 0.59 47.0 3.40e-01 89.5% 73.3%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.59 40.0 3.69e-01 71.9% 62.0%
6p2lA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 43.0 2.78e-01 82.5% 80.3%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 39.0 3.78e-01 75.4% 68.2%
2r41A00 3.10.450.150 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein 0.55 42.0 3.56e-01 84.2% 59.2%
6canA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 37.0 2.37e-01 70.2% 24.5%
2arfA00 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.55 38.0 2.81e-01 73.7% 35.2%
3nuhB03 3.10.20.690 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 36.0 3.20e-01 70.2% 42.7%
1mu5A01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.54 41.0 2.89e-01 87.7% 76.7%
2k7iA01 3.30.160.160 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YegP-like 0.54 37.0 3.94e-01 71.9% 97.9%
3ld7A00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.54 38.0 3.34e-01 75.4% 57.5%
6s8zA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.53 37.0 3.65e-01 75.4% 72.6%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 36.0 3.53e-01 75.4% 69.8%
1c9rA04 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.52 41.0 3.47e-01 93.0% 92.5%
2oxgC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.24e-01 82.5% 97.0%
1plqA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.51 38.0 2.50e-01 80.7% 62.0%
1auvB02 3.40.50.20 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 38.0 3.18e-01 86.0% 62.9%
3rr1A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 37.0 2.89e-01 80.7% 35.8%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5045263 101.1.11.0 alpha arrays › HTH › HTH › Ribbon-helix-helix 0.72 49.0 4.41e-01 71.9% 53.8%
5043942 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.70 50.0 4.57e-01 75.4% 90.7%
4869677 4967.1.1.30 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › RVT_connect 0.69 49.0 5.21e-01 75.4% 92.0%
3739414 330.1.1.3 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.67 47.0 3.92e-01 75.4% 45.7%
3611339 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.67 45.0 3.97e-01 75.4% 47.1%
1322782 2484.5.1.1 mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RVT_connect 0.66 54.0 4.11e-01 89.5% 75.0%
5022726 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.66 49.0 5.20e-01 78.9% 96.0%
3281300 4.1.1.426 beta barrels › SH3 › SH3 › SH3 › PF31188 0.64 44.0 4.31e-01 77.2% 64.6%
5023443 330.4.1.0 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 0.64 44.0 4.24e-01 71.9% 72.3%
4638787 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 43.0 3.91e-01 71.9% 58.7%
3500942 330.1.1.3 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.63 47.0 3.87e-01 82.5% 42.7%
5044375 2484.1.1.302 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.63 47.0 3.18e-01 82.5% 69.8%
4611568 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 44.0 4.05e-01 73.7% 64.0%
4216680 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 43.0 3.69e-01 71.9% 49.5%
3893915 330.1.1.3 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.62 46.0 3.59e-01 78.9% 40.0%
4552605 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.62 43.0 3.95e-01 73.7% 61.5%
4112241 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.61 45.0 3.93e-01 77.2% 68.2%
219788 244.2.1.3 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FCSD-flav_bind 0.61 47.0 4.45e-01 91.2% 98.7%
3749631 4.1.1.14 beta barrels › SH3 › SH3 › SH3 › Ribosomal_L21e 0.60 46.0 3.80e-01 84.2% 50.5%
3337433 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.60 46.0 4.20e-01 86.0% 97.5%
3497120 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 42.0 3.62e-01 75.4% 49.5%
4115704 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.60 41.0 3.76e-01 71.9% 62.7%
4040973 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.60 41.0 3.86e-01 71.9% 64.3%
3436557 220.4.1.8 beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins › ZGRF1-like_N 0.59 44.0 4.04e-01 80.7% 74.7%
222972 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.59 40.0 3.55e-01 71.9% 55.1%
4632710 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.59 40.0 4.36e-01 77.2% 91.1%
5040652 4.11.1.0 beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase 0.58 47.0 3.29e-01 91.2% 56.9%
3482014 2003.1.2.17 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Amino_oxidase 0.58 43.0 2.87e-01 84.2% 23.7%
3459205 5.1.4.156 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Ge1_WD40 0.58 40.0 2.29e-01 71.9% 55.4%
4054729 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.58 39.0 3.64e-01 71.9% 66.7%
3642022 218.1.1.2 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.57 43.0 3.63e-01 80.7% 70.0%
4158157 4.1.1.57 beta barrels › SH3 › SH3 › SH3 › EFP_N 0.57 41.0 3.96e-01 75.4% 70.8%
3503503 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.56 42.0 3.16e-01 80.7% 77.9%
5034195 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.56 41.0 4.19e-01 80.7% 96.4%
3579382 214.1.1.0 a+b two layers › SH2 › SH2 › SH2 0.55 40.0 3.34e-01 77.2% 71.0%
4962106 2.4.1.2 beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.55 39.0 3.10e-01 75.4% 34.4%
3684267 5.1.10.15 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › RPE65 0.55 40.0 3.11e-01 78.9% 36.2%
2057235 4312.1.1.5 a+b two layers › RelE-like › RelE-like › RelE-like › RelE 0.54 38.0 3.14e-01 75.4% 40.7%
2755179 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 42.0 2.73e-01 94.7% 82.5%
3822639 5.1.3.67 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.54 44.0 2.76e-01 93.0% 66.2%
3475183 2484.1.1.74 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Tex_YqgF 0.54 41.0 2.99e-01 91.2% 85.5%
3964724 3675.1.1.1 a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.54 37.0 2.75e-01 71.9% 30.3%
3597605 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 40.0 2.99e-01 86.0% 61.2%
5056110 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.53 40.0 3.11e-01 82.5% 49.6%
4034055 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.53 39.0 2.48e-01 82.5% 35.8%
4104219 4.1.1.57 beta barrels › SH3 › SH3 › SH3 › EFP_N 0.52 36.0 3.54e-01 75.4% 67.7%
4019154 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 39.0 2.47e-01 84.2% 80.3%
4026378 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 35.0 2.38e-01 71.9% 18.8%
3705016 375.1.1.5 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L44 0.51 35.0 3.08e-01 75.4% 76.8%
3618372 2484.1.1.99 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Peptidase_A17 0.51 36.0 3.06e-01 82.5% 83.3%