←Back to structures

NC_055737.1__YP_010093783.1__KNT81_gp167__00246

Bact-Vir

NC_055737.1__YP_010093783.1__KNT81_gp167__00246

Identity

Accession:
NC_055737 ↗
Kingdom:
phage

Quality

83.5 mean pLDDT

Taxonomy

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

TaxID: 2065203

Cluster

View cluster (14 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 49-101
PDB
Domain cluster: rep: NC_031020.1__YP_009279879.1__BI036_gp022__00022__D49-102
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vxzA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 38.0 3.51e-01 81.1% 43.9%
4a6dA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 39.0 3.16e-01 83.0% 31.9%
6hgcA01 3.40.532.10 Alpha Beta › 3-Layer(aba) Sandwich › Ubiquitin C-terminal Hydrolase UCH-l3 › Peptidase C12, ubiquitin carboxyl-terminal hydrolase 0.64 50.0 3.56e-01 94.3% 81.7%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 56.0 5.20e-01 100.0% 97.1%
4n06A01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.62 42.0 3.67e-01 77.4% 45.1%
5mu3B00 3.40.50.12050 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 53.0 3.84e-01 100.0% 47.9%
2c9wA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.62 52.0 4.20e-01 100.0% 61.1%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.62 52.0 4.82e-01 98.1% 91.5%
1h4rA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 46.0 3.95e-01 83.0% 67.0%
1wguA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 47.0 3.75e-01 86.8% 60.0%
3hl6A01 3.30.1300.50 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Putative mobile pathogenicity island, N-terminal domain 0.61 42.0 3.87e-01 75.5% 87.8%
3noyB02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.60 51.0 4.31e-01 100.0% 96.8%
1iv8A02 3.30.1590.10 Alpha Beta › 2-Layer Sandwich › Maltooligosyl trehalose synthase, domain 2 › Maltooligosyl trehalose synthase, domain 2 0.57 46.0 3.69e-01 94.3% 44.9%
7mi4A02 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.57 40.0 3.63e-01 84.9% 52.7%
6qp9B01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 39.0 2.35e-01 73.6% 17.8%
1v7wA01 2.70.98.40 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Glycoside hydrolase, family 65, N-terminal domain 0.57 40.0 2.54e-01 75.5% 26.8%
1yqeA01 3.40.630.50 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › AF0625-like 0.57 48.0 3.41e-01 100.0% 88.2%
3ldtA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.56 39.0 2.92e-01 73.6% 91.0%
2nn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 45.0 3.34e-01 100.0% 83.6%
3h5aD01 3.90.930.70 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.56 44.0 3.87e-01 94.3% 83.0%
3a54A01 2.40.50.340 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 41.0 3.63e-01 84.9% 76.7%
2od0A00 3.30.1460.30 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › YgaC/TfoX-N like chaperone 0.55 49.0 3.87e-01 98.1% 88.3%
5zx8A00 3.40.50.1470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidyl-tRNA hydrolase 0.55 40.0 2.83e-01 81.1% 82.8%
2jsnA00 2.30.42.40 Mainly Beta › Roll › Pdz3 Domain › 0.55 41.0 3.44e-01 83.0% 69.8%
3nvqA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 43.0 2.64e-01 98.1% 30.2%
2wb6A00 3.90.1150.90 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.53 39.0 3.18e-01 83.0% 71.9%
5jldA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 41.0 2.82e-01 100.0% 21.0%
6i18A04 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.53 42.0 3.56e-01 98.1% 85.0%
3nqhA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 42.0 2.79e-01 100.0% 91.1%
1n7vA01 2.105.10.10 Mainly Beta › 3 Propeller › Pseudo beta propeller › Pseudo beta propeller 0.53 42.0 3.08e-01 98.1% 83.1%
3bu2A02 3.30.1940.10 Alpha Beta › 2-Layer Sandwich › Nucleic acid-binding protein fold › YtpR-like 0.53 35.0 3.21e-01 96.2% 52.2%
3sfvB01 3.30.450.390 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.53 40.0 3.05e-01 86.8% 43.0%
2ljwA00 3.30.428.40 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › Protein of unknown function DUF3067 0.52 44.0 3.54e-01 94.3% 58.7%
5i92F01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 42.0 3.09e-01 98.1% 52.3%
4hs5A00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.52 43.0 3.59e-01 100.0% 78.1%
5gaeG01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.52 42.0 3.81e-01 100.0% 91.4%
3igfA02 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 39.0 3.61e-01 90.6% 62.2%
2i8dA01 3.90.1150.200 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.52 42.0 3.75e-01 96.2% 61.7%
2joiA00 3.30.310.190 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.51 42.0 3.44e-01 90.6% 85.4%
2aujD03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.51 37.0 3.64e-01 83.0% 74.2%
3oc9A00 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 0.51 44.0 2.66e-01 98.1% 75.2%
4h5bA00 3.30.1460.70 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.51 43.0 3.17e-01 98.1% 74.3%
3n7lA02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.50 42.0 2.92e-01 96.2% 44.1%
5yrzB00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.50 41.0 4.07e-01 100.0% 100.0%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4966382 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.72 58.0 5.47e-01 94.3% 72.3%
3164102 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.71 55.0 5.85e-01 84.9% 97.8%
4929483 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 53.0 4.05e-01 98.1% 38.3%
3577308 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.66 56.0 5.55e-01 98.1% 100.0%
5047657 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 53.0 5.34e-01 94.3% 96.4%
3712990 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 53.0 5.00e-01 100.0% 92.9%
5049479 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.65 36.0 2.84e-01 84.9% 26.7%
3254221 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.65 48.0 2.87e-01 81.1% 20.3%
5023931 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 52.0 4.90e-01 96.2% 75.7%
4030804 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.65 56.0 3.53e-01 100.0% 25.2%
3839226 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.64 54.0 3.66e-01 100.0% 30.7%
4826080 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 53.0 4.62e-01 92.5% 63.0%
4043415 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.64 57.0 3.33e-01 100.0% 14.1%
3887656 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.64 54.0 4.16e-01 100.0% 53.1%
3180298 4351.1.1.1 ↗ alpha arrays › ATP12-like › ATP12-like › ATP12-like › ATP12 0.64 48.0 3.06e-01 84.9% 20.7%
5026584 101.1.2.55 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpB 0.63 33.0 2.73e-01 81.1% 27.4%
4953866 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.63 52.0 3.60e-01 100.0% 46.5%
3895743 3615.1.1.7 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › CD20 0.63 48.0 3.35e-01 86.8% 26.3%
3709800 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 56.0 4.55e-01 100.0% 54.7%
3801624 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 56.0 4.52e-01 100.0% 67.0%
3972934 4312.1.1.3 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.62 49.0 4.03e-01 92.5% 47.6%
3618540 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.62 50.0 4.66e-01 100.0% 73.3%
4945301 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 46.0 3.43e-01 83.0% 31.3%
3209881 109.4.1.207 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_2 0.61 42.0 2.41e-01 73.6% 7.0%
4989457 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.61 49.0 5.03e-01 94.3% 100.0%
4424957 3804.1.1.0 ↗ alpha bundles › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain 0.61 43.0 3.01e-01 96.2% 22.2%
3784810 216.1.1.20 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UBC_like 0.60 49.0 4.22e-01 98.1% 95.8%
4023242 220.1.1.187 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › VPS13_C 0.60 43.0 3.35e-01 77.4% 45.6%
3838957 3439.1.1.0 ↗ a+b two layers › PafA/Dop C-terminal domain › PafA/Dop C-terminal domain › PafA/Dop C-terminal domain 0.58 48.0 4.47e-01 100.0% 80.0%
3512465 1.1.1.19 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Pol_BBD 0.58 45.0 3.57e-01 90.6% 92.5%
4947228 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 45.0 3.62e-01 84.9% 81.0%
3781478 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.57 46.0 3.91e-01 100.0% 81.0%
3995015 5.1.4.241 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › eIF2A 0.57 47.0 3.05e-01 96.2% 40.0%
3958912 296.1.1.0 ↗ a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 0.57 46.0 3.94e-01 100.0% 94.0%
4429302 4161.1.1.0 ↗ beta complex topology › MOSC N-terminal domain-like › MOSC N-terminal domain-like › MOSC N-terminal domain-like 0.57 48.0 3.07e-01 100.0% 24.6%
4097938 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.57 46.0 3.85e-01 100.0% 74.5%
3708118 2004.1.1.26 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.56 44.0 2.78e-01 90.6% 91.7%
4484131 4161.1.1.0 ↗ beta complex topology › MOSC N-terminal domain-like › MOSC N-terminal domain-like › MOSC N-terminal domain-like 0.56 47.0 3.00e-01 98.1% 40.4%
5075279 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 46.0 3.64e-01 94.3% 43.5%
3432581 2003.1.5.31 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GRAS 0.55 43.0 2.63e-01 88.7% 68.1%
4945871 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.55 33.0 2.79e-01 88.7% 33.7%
5012208 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.55 45.0 3.92e-01 98.1% 72.2%
3214898 5.1.11.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › eIF2A 0.55 43.0 2.60e-01 94.3% 17.7%
4954769 2498.2.1.0 ↗ mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain 0.54 45.0 3.35e-01 100.0% 51.0%
5047029 101.1.2.55 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpB 0.54 41.0 3.34e-01 84.9% 77.1%
3228787 4161.1.1.0 ↗ beta complex topology › MOSC N-terminal domain-like › MOSC N-terminal domain-like › MOSC N-terminal domain-like 0.54 44.0 2.89e-01 100.0% 24.3%
5081918 3962.1.1.0 ↗ alpha arrays › N-terminal helical domain in restriction-modification system methylation subunit-like › N-terminal helical domain in restriction-modification system methylation subunit › N-terminal helical domain in restriction-modification system methylation subunit 0.54 47.0 3.08e-01 100.0% 29.2%
3591100 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.53 41.0 2.62e-01 96.2% 87.5%
4218376 241.2.1.1 ↗ a+b two layers › Type III secretory system chaperone-like › Frataxin-like › Frataxin-like › Frataxin_Cyay 0.53 44.0 3.72e-01 100.0% 80.0%
5004736 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 39.0 3.85e-01 92.5% 74.1%
3519816 1.1.15.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like 0.53 43.0 2.89e-01 100.0% 21.7%
3802590 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.53 42.0 2.65e-01 94.3% 55.0%
3471206 63.1.1.8 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › PRKCSH, PRKCSH_1 0.53 39.0 2.93e-01 81.1% 75.9%
146926 3066.1.1.0 ↗ 0.52 39.0 3.31e-01 83.0% 60.0%
3508939 220.1.1.13 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1 0.52 37.0 2.92e-01 79.2% 70.0%
2326833 3804.1.1.0 ↗ alpha bundles › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain 0.52 44.0 3.28e-01 100.0% 57.9%
2581397 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.51 41.0 3.54e-01 98.1% 74.5%
3164780 331.22.1.2 ↗ a+b two layers › TBP-like › Outer membrane protein assembly factor BamC › Outer membrane protein assembly factor BamC › PF29358 0.51 44.0 3.05e-01 100.0% 61.5%
4260807 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.51 41.0 3.87e-01 100.0% 98.6%
4056469 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.51 39.0 2.68e-01 98.1% 25.5%
4426940 210.1.1.4 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › IMP_cyclohyd 0.51 42.0 2.97e-01 100.0% 50.8%
1918436 6051.5.1.1 ↗ alpha duplicates or obligate multimers › Docking domains in modular polyketide synthases › Class 3 N-terminal docking domain › Class 3 N-terminal docking domain › TubC_N 0.50 37.0 3.61e-01 79.2% 74.6%
3806737 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.50 41.0 3.10e-01 96.2% 59.3%