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NC_042116.1__YP_009624028.1__FDJ41_gp485__00418

Bact-Vir

NC_042116.1__YP_009624028.1__FDJ41_gp485__00418

Identity

Accession:
NC_042116 ↗
Kingdom:
phage

Quality

81.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Eneladusvirus› Yersinia_phage_fHe-Yen9-04

TaxID: 2052742

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 medium residues 55-106
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6bg2A02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.64 55.0 4.23e-01 100.0% 55.2%
3f1jA00 2.70.20.40 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Borna disease virus, matrix protein 0.62 47.0 3.55e-01 100.0% 32.1%
7snsB01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 52.0 3.77e-01 100.0% 35.2%
1r89A04 3.30.70.1550 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Archaeal tRNA CCA-adding enzyme catalytic domain 0.61 44.0 4.67e-01 80.8% 90.9%
4crsA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.61 52.0 3.95e-01 100.0% 53.0%
1omsA00 3.30.70.1050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain 0.61 50.0 4.01e-01 96.2% 93.9%
5hftD00 3.60.20.40 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Gamma-glutamyltranspeptidase, small (S) subunit 0.61 34.0 2.45e-01 100.0% 17.5%
1zysA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 51.0 4.30e-01 100.0% 69.5%
2f2uB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 52.0 3.58e-01 100.0% 37.5%
2clqA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 52.0 4.45e-01 100.0% 72.9%
2hw6A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 52.0 4.40e-01 100.0% 75.0%
4k22B01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 42.0 2.81e-01 78.8% 17.6%
2vz6B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 50.0 4.38e-01 100.0% 80.7%
2cw8A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.59 50.0 3.54e-01 100.0% 32.0%
4js8A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 50.0 4.24e-01 100.0% 76.4%
3mahA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 48.0 4.43e-01 100.0% 70.0%
1vi7A02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 39.0 3.59e-01 73.1% 90.1%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.56 42.0 3.77e-01 80.8% 57.5%
3mpoA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.55 44.0 3.68e-01 98.1% 82.2%
6gmhK00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.55 48.0 3.75e-01 100.0% 51.3%
4feuF01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 45.0 4.17e-01 100.0% 84.9%
2gysA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 45.0 3.96e-01 100.0% 74.4%
5xogK00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.55 47.0 3.73e-01 100.0% 52.2%
4lq0A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.54 44.0 3.35e-01 100.0% 43.5%
6i7dB01 6.20.240.20 Special › Other non-globular › Alpha-Beta Plaits › 0.54 42.0 4.14e-01 90.4% 91.5%
3jr1A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 45.0 3.78e-01 100.0% 63.6%
4fg9A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 48.0 4.17e-01 100.0% 72.2%
4aybL00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.53 45.0 3.81e-01 100.0% 70.3%
4aybA05 4.10.320.40 Few Secondary Structures › Irregular › Dihydrolipoamide Transferase › 0.53 37.0 3.91e-01 90.4% 88.6%
3agjF01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.52 43.0 3.37e-01 100.0% 85.0%
3kmaA00 2.170.270.10 Mainly Beta › Beta Complex › Beta-clip-like › SET domain 0.51 39.0 3.29e-01 90.4% 83.8%
3njcA00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.51 41.0 3.11e-01 100.0% 46.4%
2pa8D01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.50 42.0 3.66e-01 100.0% 61.4%
6vudA02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.50 38.0 3.59e-01 100.0% 66.7%
ECOD (66)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2084827 304.165.1.1 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 › Ta1207 0.66 56.0 3.99e-01 100.0% 32.5%
5017624 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.65 49.0 3.38e-01 96.2% 22.6%
5027068 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.63 51.0 3.38e-01 100.0% 21.4%
4935111 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.63 49.0 3.33e-01 100.0% 22.6%
4983061 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.63 53.0 3.60e-01 100.0% 25.7%
5042376 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.62 50.0 3.44e-01 100.0% 24.9%
4427444 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.62 48.0 3.25e-01 98.1% 22.0%
4931660 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.62 49.0 3.35e-01 100.0% 23.6%
4928430 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.62 50.0 3.37e-01 100.0% 22.4%
4626252 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.62 52.0 3.48e-01 98.1% 22.7%
3292735 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.62 52.0 3.96e-01 100.0% 88.1%
4988258 5104.1.1.0 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.61 51.0 3.92e-01 100.0% 40.8%
5028439 2003.1.5.50 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › TylF 0.61 49.0 3.29e-01 92.3% 82.2%
5024998 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.61 51.0 3.43e-01 98.1% 23.8%
3602169 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.60 53.0 4.53e-01 100.0% 62.4%
5051925 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.60 51.0 4.10e-01 100.0% 51.8%
3520972 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 52.0 3.13e-01 100.0% 27.4%
4995029 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.60 52.0 3.35e-01 100.0% 21.3%
3476713 601.23.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.60 52.0 3.19e-01 100.0% 15.5%
4969421 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.60 47.0 3.18e-01 100.0% 21.4%
4587247 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.59 51.0 4.32e-01 100.0% 60.0%
5070800 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.59 47.0 3.13e-01 98.1% 21.4%
5049353 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.58 48.0 3.78e-01 100.0% 53.6%
3951221 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.58 50.0 4.32e-01 100.0% 61.2%
5030884 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.58 48.0 3.25e-01 100.0% 23.8%
4958446 241.9.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › YdhG-like › YdhG-like 0.58 48.0 3.68e-01 100.0% 40.8%
5043573 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.58 51.0 3.46e-01 100.0% 28.4%
4200948 242.1.1.2 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.57 48.0 4.00e-01 100.0% 58.0%
4978271 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.57 48.0 3.22e-01 100.0% 23.2%
4970737 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.57 49.0 3.28e-01 100.0% 24.2%
5077613 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.56 49.0 3.27e-01 100.0% 23.7%
4965722 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.56 48.0 3.19e-01 98.1% 23.5%
137125 873.1.1.5 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › HNOB 0.56 48.0 3.37e-01 100.0% 34.3%
4206076 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.56 40.0 3.81e-01 78.8% 63.1%
2075999 3012.1.1.4 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Hydrolase_3 0.55 44.0 3.68e-01 98.1% 82.2%
3310571 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.55 47.0 3.20e-01 100.0% 24.8%
4627664 601.23.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.55 45.0 2.86e-01 100.0% 17.8%
4374003 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.54 44.0 3.73e-01 100.0% 70.4%
4063927 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.54 38.0 2.64e-01 76.9% 35.3%
3824583 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.54 42.0 2.99e-01 100.0% 25.8%
3601271 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.54 41.0 2.61e-01 88.5% 68.2%
4285727 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.53 39.0 3.15e-01 82.7% 40.9%
3595902 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.53 42.0 2.93e-01 100.0% 24.5%
4591467 885.1.1.1 ↗ a+b complex topology › Transcription factor NusA, N-terminal domain › Transcription factor NusA, N-terminal domain › Transcription factor NusA, N-terminal domain › NusA_N 0.53 44.0 3.44e-01 98.1% 43.2%
5021478 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.53 36.0 3.55e-01 73.1% 67.3%
3479084 12.5.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related 0.53 45.0 3.31e-01 100.0% 68.0%
3609850 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.53 42.0 2.94e-01 100.0% 24.4%
4033416 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.53 39.0 3.60e-01 80.8% 60.0%
4460221 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.53 42.0 3.59e-01 88.5% 61.2%
3590864 3012.1.1.0 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.53 40.0 3.47e-01 98.1% 82.9%
3701949 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.52 43.0 3.07e-01 100.0% 35.6%
5030922 304.24.1.37 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › MCR_C 0.52 35.0 3.36e-01 73.1% 92.3%
3164849 3016.1.1.11 ↗ 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 › SelA 0.51 44.0 3.57e-01 100.0% 61.9%
3504523 4955.1.1.0 ↗ a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.51 40.0 3.51e-01 100.0% 78.9%
4203622 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.51 40.0 2.94e-01 100.0% 28.6%
5000277 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 40.0 3.45e-01 96.2% 60.2%
3781650 2003.6.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like 0.51 42.0 2.66e-01 98.1% 96.7%
4986894 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.51 43.0 4.19e-01 100.0% 90.0%
4071991 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.51 40.0 2.89e-01 100.0% 26.5%
4051072 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 39.0 3.37e-01 88.5% 55.6%
4362064 304.117.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC 0.51 36.0 3.35e-01 78.8% 58.6%
5064038 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 0.50 38.0 3.47e-01 100.0% 59.0%
4198379 220.1.1.162 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF31014 0.50 43.0 3.11e-01 100.0% 35.6%
4138504 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.50 39.0 2.85e-01 100.0% 27.0%
4932631 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.50 39.0 3.16e-01 86.5% 48.5%
4943447 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.50 38.0 3.50e-01 88.5% 65.3%