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NC_015274.1__YP_004306911.1__StPhDp-1_gp23__00023

Bact-Vir

NC_015274.1__YP_004306911.1__StPhDp-1_gp23__00023

Identity

Accession:
NC_015274 ↗
Kingdom:
phage

Quality

93.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Streptococcus_phage_Dp-1

TaxID: 59241

Cluster

View cluster (36 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 2-88
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.83 47.0 5.87e-01 100.0% 92.5%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.73 41.0 4.32e-01 97.7% 61.3%
1nc7A00 2.60.290.11 Mainly Beta › Sandwich › Hypothetical Protein Tm1070; Chain: A › TM1070-like 0.69 41.0 3.78e-01 97.7% 44.8%
2q7nA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 42.0 4.10e-01 100.0% 55.1%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.67 37.0 3.23e-01 96.6% 36.1%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.67 41.0 3.96e-01 100.0% 55.1%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.65 43.0 4.56e-01 100.0% 76.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.65 40.0 3.96e-01 97.7% 57.6%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.64 42.0 4.46e-01 100.0% 76.3%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.64 39.0 4.30e-01 100.0% 78.8%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.61 41.0 4.06e-01 100.0% 63.5%
1ylnA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 42.0 3.83e-01 98.9% 54.4%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.60 39.0 3.50e-01 97.7% 48.7%
2npnA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.60 37.0 3.52e-01 100.0% 49.5%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.58 38.0 3.58e-01 100.0% 53.2%
1a21A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 35.0 3.41e-01 100.0% 53.1%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.58 37.0 3.87e-01 96.6% 72.7%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.57 42.0 3.81e-01 98.9% 58.0%
3ijfX00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.57 37.0 3.29e-01 97.7% 47.2%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.56 37.0 3.41e-01 97.7% 50.9%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.56 42.0 3.36e-01 100.0% 39.2%
2fr5A00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.56 37.0 3.19e-01 97.7% 42.6%
2f4nB02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.55 41.0 4.04e-01 94.3% 72.3%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 37.0 2.81e-01 100.0% 29.9%
5c50B00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.53 42.0 3.32e-01 86.2% 96.8%
1cyyA02 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.53 48.0 4.23e-01 100.0% 99.2%
4p04A01 2.60.40.3100 Mainly Beta › Sandwich › Immunoglobulin-like › Arylsulphate sulphotransferase monomer, N-terminal domain 0.52 32.0 3.05e-01 98.9% 49.1%
5u81A01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.52 36.0 2.65e-01 73.6% 73.0%
1ocsA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 39.0 3.40e-01 79.3% 90.9%
5jgfA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.52 47.0 3.94e-01 100.0% 75.9%
1mw7A02 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.52 39.0 3.95e-01 80.5% 96.6%
6x1kA01 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.51 46.0 4.16e-01 97.7% 100.0%
3bgyA00 3.20.100.10 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › mRNA triphosphatase Cet1-like 0.51 44.0 3.34e-01 100.0% 49.1%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3903752 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.77 45.0 4.19e-01 100.0% 48.6%
5053865 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.76 52.0 5.19e-01 100.0% 68.9%
5042583 10.3.1.0 ↗ beta sandwiches › jelly-roll › TNF-like › TNF-like 0.74 43.0 4.17e-01 100.0% 52.6%
5027230 10.7.1.0 ↗ beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.72 41.0 4.17e-01 97.7% 56.5%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.70 46.0 5.28e-01 100.0% 90.6%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.70 47.0 4.79e-01 100.0% 71.1%
3595506 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.70 38.0 3.35e-01 97.7% 38.3%
5014684 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.70 44.0 5.21e-01 100.0% 94.8%
4996552 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.70 46.0 4.66e-01 100.0% 68.2%
1442393 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.70 46.0 4.28e-01 100.0% 54.1%
5012981 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.69 39.0 4.02e-01 97.7% 57.6%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 45.0 4.84e-01 100.0% 77.3%
3287357 3115.3.1.0 ↗ a+b two layers › GP2-like › P56 › P56 0.69 45.0 5.38e-01 98.9% 100.0%
3218726 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.69 49.0 4.64e-01 100.0% 64.0%
5012895 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.69 43.0 5.19e-01 98.9% 100.0%
5074648 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.68 45.0 4.78e-01 100.0% 77.3%
4004704 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.68 37.0 4.74e-01 95.4% 100.0%
2831852 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 44.0 4.23e-01 100.0% 57.4%
3975705 3115.6.1.0 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon 0.68 38.0 4.75e-01 98.9% 96.0%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.67 44.0 5.19e-01 100.0% 98.3%
3489385 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 36.0 3.17e-01 100.0% 36.0%
3994984 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.67 45.0 5.11e-01 100.0% 93.8%
4160542 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 42.0 5.02e-01 98.9% 98.3%
4007508 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.66 38.0 4.76e-01 98.9% 100.0%
2512518 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 42.0 4.07e-01 100.0% 57.4%
3707942 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.64 39.0 3.53e-01 98.9% 45.2%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.63 41.0 4.73e-01 98.9% 98.3%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 41.0 4.50e-01 100.0% 82.9%
3508990 3115.3.1.2 ↗ a+b two layers › GP2-like › P56 › P56 › DUF2922 0.62 44.0 4.90e-01 97.7% 100.0%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.62 41.0 4.63e-01 100.0% 98.3%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.62 40.0 4.50e-01 100.0% 92.1%
4175430 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.61 42.0 3.05e-01 100.0% 25.1%
5023452 303.1.1.1 ↗ a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.61 45.0 3.79e-01 100.0% 46.9%
5037200 303.1.1.1 ↗ a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.61 45.0 3.70e-01 100.0% 44.2%
4654177 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.61 39.0 2.86e-01 100.0% 23.3%
3510040 3115.3.1.2 ↗ a+b two layers › GP2-like › P56 › P56 › DUF2922 0.58 41.0 4.24e-01 97.7% 80.0%
3603541 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 39.0 3.87e-01 100.0% 67.8%
3259237 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.56 46.0 4.83e-01 100.0% 95.0%
4368632 10.32.1.266 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GldH_lipo 0.56 42.0 3.54e-01 100.0% 48.9%
3190590 11.1.1.14 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Glyco_hydro_2 0.55 38.0 3.54e-01 100.0% 57.3%
3509583 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.53 47.0 4.26e-01 98.9% 99.2%
None — 0.53 48.0 3.17e-01 100.0% 36.4%
3744424 312.1.1.6 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › CwfJ_C_2,CwfJ_C_1 0.53 37.0 2.84e-01 74.7% 54.0%
4263801 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.52 41.0 2.37e-01 100.0% 9.4%
4487057 4007.1.1.1 ↗ a+b two layers › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › Transcrip_reg 0.52 40.0 4.01e-01 82.8% 94.4%
3388281 3019.1.1.0 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain 0.51 43.0 3.42e-01 97.7% 46.5%
3489258 306.8.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › TM1457-like › TM1457-like 0.50 37.0 3.46e-01 75.9% 82.9%
3618846 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.50 39.0 2.63e-01 100.0% 21.1%