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NC_055737.1__YP_010093588.1__KNT81_gp051__00051

Bact-Vir

NC_055737.1__YP_010093588.1__KNT81_gp051__00051

Identity

Accession:
NC_055737 ↗
Kingdom:
phage

Quality

80.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Bragavirus› Proteus_phage_phiP4-3

TaxID: 2065203

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 13-82
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4l9cA00 3.40.1000.30 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › 0.73 53.0 4.14e-01 77.1% 58.0%
1ah5A03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.70 50.0 4.74e-01 77.1% 68.6%
2rqlA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.64 45.0 4.15e-01 74.3% 63.2%
5z1gB01 3.40.50.10480 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Brix domain 0.64 55.0 4.02e-01 100.0% 77.5%
1uokA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.63 44.0 4.29e-01 72.9% 100.0%
4r80A00 3.10.450.630 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 44.0 4.31e-01 75.7% 69.7%
1lf7A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 50.0 3.84e-01 91.4% 39.6%
1vprA03 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.60 54.0 4.14e-01 100.0% 51.0%
4g3vA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.59 51.0 3.98e-01 100.0% 93.2%
4n6qA00 2.60.40.3960 Mainly Beta › Sandwich › Immunoglobulin-like › Velvet domain 0.58 50.0 3.81e-01 100.0% 74.7%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 36.0 3.60e-01 72.9% 62.0%
4nkbA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.56 45.0 3.85e-01 88.6% 77.2%
3v6oB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 49.0 4.39e-01 100.0% 93.0%
3fc7A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 40.0 3.61e-01 81.4% 54.0%
8gq6A01 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.55 39.0 2.64e-01 75.7% 24.2%
2n1kA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 50.0 4.35e-01 100.0% 79.2%
2fpnA01 3.30.2030.10 Alpha Beta › 2-Layer Sandwich › TBP-like › YwmB-like 0.55 41.0 3.43e-01 100.0% 42.1%
3htyA00 2.40.128.280 Mainly Beta › Beta Barrel › Lipocalin › 0.55 40.0 3.69e-01 78.6% 75.5%
4fh3A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 46.0 3.93e-01 100.0% 77.6%
2nvmA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.55 39.0 3.54e-01 78.6% 57.7%
2l2nA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 38.0 3.86e-01 100.0% 71.8%
2jheA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 43.0 3.76e-01 87.1% 66.7%
3l5iA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 48.0 4.49e-01 98.6% 96.6%
3qkgA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 48.0 3.64e-01 98.6% 65.2%
2qmiA02 2.40.128.210 Mainly Beta › Beta Barrel › Lipocalin › Pab87 octamerisation domain 0.54 39.0 3.52e-01 77.1% 82.0%
1kvzA00 3.10.130.10 Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain 0.54 40.0 3.50e-01 80.0% 66.4%
3r8qA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 48.0 4.43e-01 100.0% 91.1%
1fnfA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 48.0 4.35e-01 100.0% 91.5%
1pbyB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 39.0 2.58e-01 78.6% 49.0%
7ne4A01 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.53 37.0 2.51e-01 75.7% 30.4%
3m2tA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 45.0 3.63e-01 100.0% 51.3%
1bquA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 48.0 4.24e-01 100.0% 85.0%
3holA03 2.40.128.240 Mainly Beta › Beta Barrel › Lipocalin › 0.53 45.0 4.26e-01 100.0% 94.4%
3b5hA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 36.0 3.45e-01 81.4% 59.8%
6j8yC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.53 47.0 3.21e-01 100.0% 92.2%
3r8qA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 47.0 4.33e-01 100.0% 90.2%
4meaA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 46.0 3.01e-01 100.0% 30.9%
2v5yA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 47.0 4.14e-01 100.0% 90.2%
5llwA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 38.0 3.54e-01 78.6% 67.4%
1lfoA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 47.0 3.88e-01 100.0% 84.3%
1orvA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 46.0 3.17e-01 100.0% 44.2%
3q0xA01 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.52 45.0 3.52e-01 97.1% 85.8%
1n26A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 45.0 4.01e-01 100.0% 86.0%
3wi7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 45.0 3.04e-01 100.0% 58.8%
2y3vD00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.52 44.0 3.49e-01 97.1% 89.6%
1vyfA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 45.0 3.71e-01 100.0% 65.9%
1qw2A00 3.30.1980.10 Alpha Beta › 2-Layer Sandwich › Hypothetical protein Ta1206 fold › Hypothetical protein YunC 0.52 37.0 3.33e-01 77.1% 62.7%
5z5dA02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 39.0 2.90e-01 91.4% 29.6%
1fu1A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.51 44.0 3.75e-01 97.1% 79.7%
1edqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.86e-01 100.0% 93.5%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.51 44.0 3.55e-01 98.6% 69.2%
6u7jA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 44.0 4.12e-01 100.0% 94.4%
2avdA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 38.0 2.69e-01 80.0% 71.2%
4q66A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 44.0 4.08e-01 100.0% 89.1%
3h27A00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.51 42.0 2.67e-01 98.6% 72.7%
2hnkA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 38.0 2.73e-01 84.3% 36.7%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3897425 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.77 63.0 5.87e-01 100.0% 71.8%
4890953 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.76 63.0 5.75e-01 100.0% 68.1%
3488996 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.76 63.0 5.87e-01 100.0% 72.9%
3929562 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.75 60.0 5.66e-01 100.0% 71.4%
4990916 283.2.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.75 67.0 5.97e-01 100.0% 79.0%
2779098 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.75 62.0 5.75e-01 100.0% 71.3%
4157358 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 0.75 51.0 4.99e-01 71.4% 67.9%
3497368 864.1.1.1 ↗ a+b two layers › DLC › DLC › DLC › Dynein_light 0.74 61.0 5.73e-01 100.0% 72.9%
5028178 283.2.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.73 64.0 4.63e-01 100.0% 65.4%
4336488 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 0.73 49.0 4.96e-01 70.0% 74.3%
3957486 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.72 52.0 4.36e-01 77.1% 79.2%
4359254 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 0.68 49.0 4.83e-01 77.1% 76.0%
4941364 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.68 48.0 4.22e-01 74.3% 59.0%
4087213 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 0.66 46.0 4.56e-01 74.3% 74.7%
4969909 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.66 48.0 3.79e-01 87.1% 36.7%
3963078 283.1.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase 0.65 54.0 5.18e-01 100.0% 80.0%
3615406 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 45.0 4.03e-01 85.7% 52.0%
4988629 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.63 40.0 2.68e-01 72.9% 15.8%
3809302 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.62 41.0 3.88e-01 98.6% 56.5%
5053654 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 43.0 3.69e-01 87.1% 44.2%
5053021 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.60 39.0 3.67e-01 71.4% 52.2%
4969245 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.60 44.0 3.37e-01 77.1% 49.7%
5011728 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.60 39.0 3.56e-01 74.3% 49.5%
5012403 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 52.0 3.99e-01 100.0% 51.5%
1873865 216.1.1.6 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UFC1 0.59 47.0 3.66e-01 90.0% 44.3%
4937717 2011.1.1.6 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20 0.59 50.0 3.55e-01 100.0% 90.4%
3417117 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.58 38.0 2.50e-01 74.3% 14.2%
3742859 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 0.57 41.0 4.28e-01 100.0% 88.3%
3615490 312.1.1.23 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › GDH_2nd 0.57 45.0 3.42e-01 91.4% 43.7%
4021333 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 46.0 3.15e-01 100.0% 79.0%
4999520 2008.1.1.44 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › FokI_cleav_dom 0.55 42.0 3.35e-01 88.6% 41.2%
3243889 9.1.1.12 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › THAP4_heme-bd 0.55 48.0 3.57e-01 100.0% 82.2%
4972327 4312.1.1.0 ↗ a+b two layers › RelE-like › RelE-like › RelE-like 0.55 38.0 3.45e-01 72.9% 58.9%
3994973 101.1.12.3 ↗ alpha arrays › HTH › HTH › HTH motif inserted in other structures › SAS-6_N 0.55 46.0 3.81e-01 95.7% 97.7%
4997576 223.1.1.27 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_10 0.54 42.0 3.68e-01 85.7% 68.2%
3838516 246.1.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.54 46.0 3.20e-01 100.0% 31.7%
1693530 225.3.1.1 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › Virion egress protein UL31 homolog › Virion egress protein UL31 homolog › Herpes_UL31 0.54 45.0 3.20e-01 94.3% 49.1%
5067842 223.1.1.27 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_10 0.54 41.0 3.37e-01 85.7% 54.3%
4463632 4312.1.1.3 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.54 40.0 3.79e-01 87.1% 65.6%
3373320 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.53 36.0 3.67e-01 100.0% 70.0%
3962450 9.27.1.0 ↗ beta barrels › Lipocalins/Streptavidin › LpqH › LpqH 0.53 48.0 4.19e-01 100.0% 70.5%
3589620 4312.1.1.11 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE-like_toxin 0.53 42.0 3.95e-01 88.6% 68.9%
3929905 328.1.1.1 ↗ a+b two layers › IF3-like › AlbA-like › AlbA-like › Alba 0.53 39.0 3.41e-01 82.9% 83.3%
3881671 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.53 45.0 3.85e-01 97.1% 84.2%
3560523 11.1.1.178 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_2 0.53 45.0 4.03e-01 100.0% 91.4%
4998404 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 41.0 4.39e-01 100.0% 95.0%
3897033 372.2.1.1 ↗ a+b complex topology › RNase A-like › EndoU-like › EndoU-like › XendoU 0.53 46.0 3.08e-01 100.0% 98.2%
3953943 9.27.1.1 ↗ beta barrels › Lipocalins/Streptavidin › LpqH › LpqH › Myco_19_kDa 0.53 47.0 4.06e-01 100.0% 67.3%
4937627 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 41.0 3.83e-01 87.1% 88.9%
3386772 246.1.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.52 44.0 3.11e-01 100.0% 32.6%
3553623 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.52 45.0 3.78e-01 98.6% 79.2%
3550970 719.1.1.5 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › PF27933 0.52 45.0 3.94e-01 100.0% 83.6%
3509569 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.52 43.0 3.75e-01 100.0% 60.0%
3731818 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.52 44.0 2.77e-01 97.1% 30.1%
4544637 4312.1.1.3 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.51 39.0 3.67e-01 90.0% 65.6%
3767960 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.51 44.0 3.69e-01 98.6% 83.2%
3804630 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 39.0 3.32e-01 85.7% 50.4%
3740897 5.1.4.36 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › MMS1_N 0.51 39.0 2.56e-01 85.7% 77.0%
None — 0.51 42.0 3.11e-01 97.1% 85.9%
4966333 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.50 36.0 3.73e-01 78.6% 86.2%
5026576 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.50 42.0 3.94e-01 98.6% 75.3%