←Back to structures

NC_049345.1__YP_009874046.1__HYO70_gp54__00054

Bact-Vir

NC_049345.1__YP_009874046.1__HYO70_gp54__00054

Identity

Accession:
NC_049345 ↗
Kingdom:
phage

Quality

73.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Plymouthvirus› Roseovarius_Plymouth_podovirus_1

TaxID: 926474

Cluster

Singleton — not in a non-trivial cluster

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 5-71
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fsdA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.70 47.0 3.83e-01 70.1% 40.5%
5bkaE01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.68 47.0 3.69e-01 71.6% 37.9%
6kjuB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.68 43.0 3.56e-01 76.1% 37.6%
3cj1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 55.0 4.18e-01 91.0% 46.8%
2owpA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.66 43.0 3.50e-01 70.1% 34.9%
4pswB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.63 49.0 3.13e-01 86.6% 21.0%
2giaA00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.63 50.0 3.92e-01 89.6% 63.6%
1zj8A04 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.61 53.0 4.15e-01 98.5% 56.1%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.61 46.0 4.44e-01 92.5% 70.9%
3ga4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 49.0 3.78e-01 91.0% 76.3%
1x6cA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 47.0 3.99e-01 88.1% 59.3%
5uaiA01 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.60 50.0 3.58e-01 94.0% 35.9%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.59 43.0 3.40e-01 92.5% 35.6%
2hqsA01 3.40.50.10070 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › TolB, N-terminal domain 0.57 48.0 3.82e-01 95.5% 50.7%
2pk0A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.57 49.0 3.39e-01 100.0% 85.8%
3lydA01 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.57 46.0 3.68e-01 92.5% 43.7%
1gm5A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 43.0 3.84e-01 85.1% 88.2%
2pi2D00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 46.0 3.90e-01 98.5% 91.9%
4gf3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.55 45.0 3.70e-01 91.0% 68.3%
2qkdA01 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.54 31.0 3.58e-01 70.1% 77.1%
4ojdH01 2.60.98.60 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Cell-cell fusogen EFF/AFF, domain 1 0.54 45.0 3.44e-01 97.0% 70.7%
2xsgB01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 42.0 2.87e-01 91.0% 32.6%
3r0qA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.53 44.0 3.26e-01 98.5% 85.6%
4fekB00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 43.0 2.91e-01 88.1% 36.7%
2q2eB01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.53 44.0 3.21e-01 100.0% 76.9%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.52 42.0 3.56e-01 98.5% 67.4%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 45.0 3.00e-01 95.5% 58.5%
8adlB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 39.0 2.61e-01 85.1% 17.9%
5ay6A01 2.60.98.20 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Flagellar hook protein FlgE 0.52 41.0 3.15e-01 91.0% 59.1%
5aj3Q00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 37.0 3.18e-01 76.1% 81.7%
2cwaA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 44.0 3.84e-01 98.5% 78.0%
3qsjA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.52 40.0 2.90e-01 89.6% 84.2%
2vzsA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.78e-01 94.0% 88.1%
1mu5A01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.51 42.0 3.13e-01 100.0% 78.1%
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 40.0 4.14e-01 92.5% 100.0%
3iveA01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.51 37.0 2.48e-01 79.1% 93.1%
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 0.51 37.0 3.60e-01 79.1% 87.8%
1ffvB04 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.50 37.0 2.81e-01 83.6% 54.5%
2yq2A02 2.60.40.3000 Mainly Beta › Sandwich › Immunoglobulin-like › Pestivirus envelope glycoprotein E2, domain B 0.50 38.0 3.66e-01 80.6% 76.3%
ECOD (70)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3613469 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.79 72.0 5.53e-01 98.5% 65.0%
4986976 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.70 48.0 3.92e-01 80.6% 40.0%
3502799 5.1.4.15 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › RPE65 0.70 61.0 3.65e-01 100.0% 39.2%
3444177 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.70 61.0 5.77e-01 100.0% 81.2%
3606828 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.68 54.0 4.33e-01 86.6% 52.3%
3710326 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 58.0 5.34e-01 98.5% 76.5%
3878170 5.1.4.549 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF28327 0.66 57.0 3.68e-01 100.0% 20.0%
3805832 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.66 57.0 3.57e-01 95.5% 36.2%
3600093 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.66 52.0 4.20e-01 88.1% 51.1%
4002282 2484.1.1.15 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › GDA1_CD39 0.66 55.0 4.00e-01 94.0% 38.4%
3751112 223.2.1.29 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › DENND11 0.65 51.0 3.87e-01 88.1% 37.3%
3607858 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 55.0 4.86e-01 100.0% 66.7%
3678781 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.65 57.0 3.21e-01 97.0% 23.5%
5024957 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.65 54.0 5.18e-01 94.0% 82.3%
5041269 223.1.1.24 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_8 0.64 40.0 3.29e-01 71.6% 35.8%
3704402 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 51.0 4.43e-01 97.0% 63.5%
3406375 223.1.1.29 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_11 0.62 49.0 3.61e-01 89.6% 32.2%
4952184 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.62 39.0 3.15e-01 70.1% 34.4%
4997159 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.61 44.0 3.45e-01 76.1% 35.2%
3508989 2484.1.1.230 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27073 0.61 50.0 3.94e-01 95.5% 60.0%
5013867 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.61 43.0 3.97e-01 86.6% 58.8%
3273272 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.61 45.0 2.79e-01 79.1% 32.1%
5044314 3203.1.1.0 ↗ a+b two layers › Putative oxidoreductase › Putative oxidoreductase › Putative oxidoreductase 0.60 49.0 4.42e-01 88.1% 90.0%
3510862 5.1.4.173 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR75_2nd 0.60 52.0 3.28e-01 98.5% 38.1%
3387833 7503.1.1.7 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › LpoB 0.60 43.0 3.20e-01 74.6% 31.2%
3552839 11.1.1.795 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › FANCAA 0.60 43.0 3.63e-01 74.6% 100.0%
3259407 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 48.0 4.49e-01 95.5% 69.4%
3791149 5.1.3.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › WD40 0.60 53.0 3.33e-01 100.0% 34.4%
5067796 7575.1.1.4 ↗ a/b three-layered sandwiches › Caspase-like › Caspase-like › Caspase-like › Peptidase_C11 0.59 50.0 3.19e-01 97.0% 30.4%
3672264 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.59 54.0 3.22e-01 100.0% 34.2%
3185161 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.59 48.0 3.15e-01 92.5% 57.1%
3413200 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 49.0 3.03e-01 98.5% 14.8%
3220090 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.58 51.0 3.07e-01 100.0% 25.6%
3517477 2484.1.1.230 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27073 0.58 48.0 4.30e-01 100.0% 89.5%
3651732 2484.1.1.157 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.58 47.0 3.24e-01 95.5% 35.6%
3641990 295.1.1.39 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › DUF4371 0.58 46.0 4.54e-01 92.5% 94.7%
3614844 220.1.1.15 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › BBL5 0.57 48.0 3.88e-01 97.0% 48.6%
3924083 2484.1.1.204 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27046, PF27073 0.57 49.0 3.74e-01 100.0% 55.3%
4037556 504.1.1.1 ↗ a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › SecB 0.57 47.0 3.71e-01 91.0% 65.0%
3882304 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 45.0 3.87e-01 92.5% 52.7%
4939729 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.57 40.0 3.29e-01 80.6% 40.0%
3761570 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.57 45.0 3.79e-01 92.5% 50.4%
3701091 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 50.0 3.80e-01 100.0% 81.2%
3743583 109.21.1.4 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Sec16_C,Sec16 0.57 41.0 2.51e-01 77.6% 61.4%
3763650 5.1.4.276 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_WDR75_2nd 0.56 49.0 3.13e-01 100.0% 36.6%
3443030 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 44.0 4.17e-01 88.1% 71.2%
3507177 2484.1.1.204 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27046, PF27073 0.56 46.0 2.88e-01 94.0% 15.5%
3504143 2484.1.1.230 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27073 0.56 46.0 3.61e-01 97.0% 58.7%
4022963 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 48.0 2.88e-01 94.0% 42.0%
3436242 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 46.0 3.66e-01 98.5% 82.6%
3887745 220.1.1.149 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF4551 0.56 46.0 3.73e-01 97.0% 52.9%
3451695 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 47.0 4.23e-01 92.5% 68.9%
3933099 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.55 43.0 4.06e-01 88.1% 77.6%
3673690 331.4.1.23 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › Coatomer_b_Cpla 0.55 43.0 3.46e-01 83.6% 88.0%
3527706 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 46.0 3.77e-01 98.5% 89.6%
5046708 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.55 43.0 3.49e-01 89.6% 43.7%
3473974 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.55 46.0 3.69e-01 97.0% 95.9%
3658408 4325.1.1.13 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF4371 0.54 43.0 4.26e-01 94.0% 92.0%
3490309 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 45.0 3.71e-01 98.5% 91.9%
5000734 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 41.0 3.69e-01 86.6% 100.0%
4963083 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.53 46.0 3.31e-01 100.0% 82.3%
3562870 2484.1.1.204 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27046, PF27073 0.53 44.0 2.69e-01 98.5% 13.1%
3998607 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.53 44.0 3.51e-01 92.5% 70.5%
3210459 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 45.0 3.28e-01 97.0% 37.8%
3185173 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.51 43.0 2.72e-01 98.5% 77.1%
4579381 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.51 38.0 3.06e-01 92.5% 36.3%
3496143 4026.1.1.0 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) 0.51 45.0 3.52e-01 100.0% 86.2%
3495082 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.51 41.0 3.42e-01 92.5% 92.0%
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 0.51 36.0 3.57e-01 79.1% 85.3%
3721305 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.50 42.0 3.73e-01 97.0% 86.4%