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NC_042056.1__YP_009617165.1__FDI85_gp036__00239

Bact-Vir

NC_042056.1__YP_009617165.1__FDI85_gp036__00239

Identity

Accession:
NC_042056 ↗
Kingdom:
phage

Quality

76.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Machinavirus› Erwinia_phage_Machina

TaxID: 1883375

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 high residues 3-75
PDB
Domain cluster: rep: BML_08182015_6_5m_scaffold_7_prodigal-single.1__X__X__00200__D2-69
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.61 45.0 3.89e-01 79.5% 57.9%
2ichA01 2.40.370.10 Mainly Beta › Beta Barrel › AttH-like fold › AttH-like domain 0.56 42.0 3.19e-01 80.8% 95.0%
4d8oA03 2.60.40.2660 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 46.0 3.96e-01 100.0% 69.0%
3cqfA03 3.40.30.40 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Perfringolysin 0.52 39.0 3.40e-01 100.0% 50.8%
1konA02 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.52 46.0 4.29e-01 100.0% 88.9%
1y60A00 3.30.230.60 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › Formaldehyde-activating enzyme 0.51 42.0 3.39e-01 98.6% 76.2%
1mw7A02 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.51 44.0 4.21e-01 98.6% 98.9%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.73 53.0 5.89e-01 75.3% 100.0%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.72 53.0 5.70e-01 78.1% 93.8%
4055235 2484.1.1.41 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › AnmK 0.59 41.0 2.96e-01 74.0% 49.5%
3898503 11.1.6.5 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › UPA domain › UPA-FIIND 0.58 50.0 4.15e-01 100.0% 74.1%
3727747 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 41.0 3.48e-01 83.6% 70.4%
3218109 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 0.53 47.0 4.39e-01 98.6% 98.9%
4151818 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 0.53 47.0 4.43e-01 100.0% 96.7%
3786945 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 46.0 4.22e-01 98.6% 91.6%
3503254 4007.1.1.0 ↗ 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 0.52 45.0 4.36e-01 98.6% 100.0%
3989300 821.1.1.3 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › T5orf172 0.51 44.0 3.90e-01 100.0% 80.9%
3939531 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.51 35.0 3.17e-01 74.0% 89.1%
D2 high residues 84-260
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3djwA00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.70 26.0 3.64e-01 88.7% 66.3%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.62 29.0 3.44e-01 97.7% 63.1%
2h36X00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 24.0 2.96e-01 91.0% 57.4%
5aj3Q00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 26.0 3.29e-01 85.3% 68.8%
4wnoA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 23.0 3.25e-01 99.4% 80.5%
4ccvA00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 29.0 3.45e-01 96.0% 84.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2659065 265.1.1.3 ↗ a+b two layers › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › AP205_coat 0.61 29.0 3.77e-01 97.2% 79.2%
3515333 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 29.0 3.85e-01 94.4% 100.0%
3608988 241.4.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Hypothetical protein c14orf129, hspc210 › Hypothetical protein c14orf129, hspc210 0.54 29.0 3.75e-01 92.1% 94.7%
3935161 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.53 29.0 3.64e-01 97.7% 88.6%
4422705 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.52 27.0 3.40e-01 97.2% 81.9%
3965232 897.2.1.2 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Protein E › Protein E › CNP1 0.51 26.0 2.95e-01 97.2% 59.3%
3924081 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.50 29.0 3.27e-01 84.7% 70.7%
3937044 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.50 27.0 3.54e-01 94.9% 94.7%