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NC_042116.1__YP_009624079.1__FDJ41_gp434__00469

Bact-Vir

NC_042116.1__YP_009624079.1__FDJ41_gp434__00469

Identity

Accession:
NC_042116 ↗
Kingdom:
phage

Quality

84.3 mean pLDDT

Taxonomy

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

TaxID: 2052742

Cluster

View cluster (4 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 47-94
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.76 66.0 5.83e-01 100.0% 73.2%
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.65 57.0 4.85e-01 100.0% 66.3%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.63 52.0 4.02e-01 100.0% 44.6%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.63 54.0 4.04e-01 100.0% 43.4%
7vbnL01 3.30.160.190 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › atu1810 like domain 0.62 49.0 4.11e-01 95.8% 70.5%
2dt8A02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.61 53.0 3.91e-01 100.0% 48.5%
2g7zA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.61 49.0 3.86e-01 100.0% 48.3%
1iv0A00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.56 45.0 3.78e-01 100.0% 49.0%
3df7A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 38.0 2.83e-01 70.8% 27.7%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.55 45.0 3.53e-01 100.0% 40.2%
2kbsA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.55 44.0 3.74e-01 100.0% 66.3%
1x49A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 43.0 3.98e-01 97.9% 75.7%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 44.0 3.44e-01 100.0% 40.5%
6n9aB02 3.30.420.200 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.53 39.0 3.63e-01 87.5% 66.7%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 40.0 3.76e-01 100.0% 65.2%
3buxB03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.53 41.0 3.59e-01 95.8% 57.0%
3fogA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 40.0 3.40e-01 100.0% 84.3%
2yx6D01 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.52 37.0 3.17e-01 87.5% 59.8%
2kw4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 41.0 3.09e-01 100.0% 38.1%
5c3vA01 3.30.800.10 Alpha Beta › 2-Layer Sandwich › Phosphatidylinositol Phosphate Kinase II Beta › Phosphatidylinositol Phosphate Kinase II Beta 0.51 41.0 2.95e-01 100.0% 59.9%
1kczA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 41.0 3.03e-01 100.0% 85.9%
3s27B01 3.10.450.330 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 38.0 2.85e-01 85.4% 84.2%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3954708 4325.1.1.9 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › PF26003 0.72 61.0 6.06e-01 100.0% 92.0%
5075465 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.69 58.0 5.45e-01 100.0% 78.3%
4188237 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.68 57.0 5.54e-01 100.0% 85.5%
4946414 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.68 58.0 4.35e-01 100.0% 51.2%
7726 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.66 56.0 5.29e-01 100.0% 81.0%
4341865 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.66 54.0 5.26e-01 100.0% 85.5%
3873956 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.65 54.0 4.11e-01 100.0% 38.3%
3281041 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.65 55.0 4.12e-01 100.0% 48.5%
4376573 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.65 54.0 4.12e-01 100.0% 51.6%
3705941 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 52.0 4.60e-01 100.0% 66.3%
4976249 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 50.0 3.90e-01 100.0% 37.4%
4944129 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.64 54.0 4.07e-01 100.0% 48.5%
3962875 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.64 55.0 4.05e-01 100.0% 48.5%
4134161 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.63 53.0 3.92e-01 100.0% 47.4%
4944904 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.63 53.0 3.94e-01 100.0% 46.7%
3606311 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 52.0 4.58e-01 100.0% 62.7%
2162577 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.62 52.0 3.90e-01 100.0% 47.0%
3990109 2484.1.1.102 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_ISL3 0.62 50.0 3.81e-01 100.0% 35.6%
5011985 2484.2.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain 0.62 49.0 4.43e-01 100.0% 62.9%
4964912 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.61 49.0 3.56e-01 100.0% 78.8%
4029631 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.61 51.0 4.03e-01 97.9% 44.8%
4944466 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.61 50.0 3.83e-01 100.0% 51.2%
4944430 244.3.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU 0.60 48.0 4.27e-01 100.0% 62.5%
4944011 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.60 51.0 4.23e-01 100.0% 54.4%
3720304 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.60 46.0 4.65e-01 100.0% 90.0%
4043193 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.59 47.0 3.72e-01 93.8% 41.8%
4370556 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.59 47.0 3.66e-01 100.0% 49.2%
3422528 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 49.0 4.63e-01 100.0% 81.7%
3935079 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 47.0 4.35e-01 100.0% 72.3%
3273505 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 44.0 3.98e-01 100.0% 65.0%
3718455 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.57 47.0 3.72e-01 100.0% 71.9%
4369577 3604.1.1.1 ↗ a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.57 38.0 3.57e-01 70.8% 55.0%
3347210 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 46.0 3.91e-01 97.9% 54.5%
3421657 5.1.10.3 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › DUF295 0.56 44.0 3.76e-01 91.7% 80.0%
5081740 2484.1.1.342 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF29288 0.56 44.0 3.18e-01 95.8% 27.9%
3930408 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.56 43.0 3.92e-01 100.0% 81.2%
4971732 1001.1.1.0 ↗ a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 0.55 38.0 3.72e-01 75.0% 74.5%
4990438 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 40.0 3.16e-01 87.5% 33.6%
3478713 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.54 43.0 3.41e-01 100.0% 40.8%
4052313 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.53 41.0 3.41e-01 95.8% 50.5%
3242138 4.8.1.1 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.53 39.0 3.71e-01 79.2% 70.0%
5040710 2484.1.1.139 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF429 0.53 45.0 2.98e-01 100.0% 95.4%
3669022 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 43.0 3.58e-01 97.9% 51.6%
3788141 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.52 40.0 3.70e-01 100.0% 66.7%
3990293 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.52 38.0 3.74e-01 87.5% 72.7%
3890480 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.52 41.0 3.64e-01 100.0% 60.0%
3927652 2484.5.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase 0.52 41.0 3.31e-01 95.8% 42.7%
3499437 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.51 40.0 2.61e-01 93.8% 29.4%