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SRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00340
Bact-VirSRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00340
Identity
- Kingdom:
- phage
Quality
64.1
mean pLDDT
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 81-226
Domain cluster:
rep: NC_048757.1__YP_009844891.1__HWC13_gp082__00082__D259-407
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03734.20 best | YkuD | 39.2 | 1.50e-09 | 83.6% | 99.3% |
CATH (27)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2mtzA02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.84 | 63.0 | 6.96e-01 | 86.3% | 94.1% |
| 4z7aA03 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.82 | 64.0 | 6.81e-01 | 84.2% | 89.3% |
| 4lpqA02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.80 | 68.0 | 7.29e-01 | 93.2% | 99.2% |
| 3tx4A02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.79 | 65.0 | 6.64e-01 | 84.2% | 89.4% |
| 6xj6A01 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.77 | 67.0 | 6.53e-01 | 91.1% | 92.3% |
| 3obyA02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.71 | 30.0 | 3.45e-01 | 84.9% | 51.4% |
| 3hrgA02 | 3.30.420.260 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain | 0.71 | 37.0 | 4.21e-01 | 98.6% | 65.8% |
| 4gniA03 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.67 | 30.0 | 3.88e-01 | 86.3% | 71.3% |
| 2vgnA02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.65 | 32.0 | 3.40e-01 | 84.2% | 52.0% |
| 2qi2A02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.65 | 30.0 | 3.40e-01 | 85.6% | 55.3% |
| 3weeA02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.62 | 35.0 | 3.46e-01 | 92.5% | 51.0% |
| 1ilyA00 | 3.30.420.100 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › | 0.62 | 30.0 | 3.77e-01 | 84.2% | 74.4% |
| 1ci3M02 | 2.40.50.100 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain | 0.61 | 24.0 | 3.64e-01 | 76.0% | 89.7% |
| 1dt9A02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.60 | 28.0 | 3.20e-01 | 84.9% | 55.4% |
| 2xzmK00 | 3.30.420.80 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribosomal protein S11/S14 | 0.59 | 31.0 | 3.19e-01 | 84.9% | 51.4% |
| 2kc8A00 | 3.30.2310.20 | Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like | 0.58 | 32.0 | 3.90e-01 | 87.7% | 83.2% |
| 3agkA02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.57 | 31.0 | 3.35e-01 | 84.9% | 60.5% |
| 3obwA02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.55 | 29.0 | 3.16e-01 | 84.9% | 58.5% |
| 3wxmB02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.54 | 29.0 | 3.15e-01 | 84.2% | 59.0% |
| 1yqfB00 | 3.10.280.10 | Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein | 0.54 | 29.0 | 2.78e-01 | 83.6% | 42.4% |
| 1okjB01 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.54 | 26.0 | 2.81e-01 | 85.6% | 50.4% |
| 4fo0A01 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.53 | 31.0 | 3.03e-01 | 85.6% | 50.0% |
| 1e8oA00 | 3.30.720.10 | Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 | 0.52 | 25.0 | 3.43e-01 | 95.2% | 90.5% |
| 2j3wC00 | 3.30.450.70 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › | 0.51 | 31.0 | 3.30e-01 | 94.5% | 65.9% |
| 4af1A02 | 3.30.420.60 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 | 0.51 | 30.0 | 3.26e-01 | 84.2% | 66.7% |
| 4h0pA01 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.50 | 33.0 | 2.91e-01 | 84.2% | 46.6% |
| 2cs0A01 | 3.30.505.10 | Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain | 0.50 | 31.0 | 3.64e-01 | 94.5% | 91.6% |
ECOD (58)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1498421 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.85 | 77.0 | 7.73e-01 | 100.0% | 93.8% |
| 4410211 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.81 | 67.0 | 7.12e-01 | 84.2% | 99.2% |
| 4302389 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.80 | 65.0 | 6.71e-01 | 83.6% | 90.6% |
| 3964337 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.78 | 68.0 | 5.97e-01 | 90.4% | 68.5% |
| 2724185 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.77 | 71.0 | 6.91e-01 | 95.9% | 94.2% |
| 2722109 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.77 | 67.0 | 6.34e-01 | 91.1% | 85.2% |
| 1684827 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.76 | 68.0 | 6.82e-01 | 93.2% | 97.9% |
| 3980648 | 4091.1.1.1 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD | 0.75 | 61.0 | 5.49e-01 | 84.2% | 68.4% |
| 3974213 | 4091.1.1.0 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.73 | 65.0 | 6.54e-01 | 91.8% | 96.6% |
| None | — | 0.73 | 66.0 | 6.60e-01 | 94.5% | 94.7% | |
| 3289583 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.68 | 36.0 | 4.10e-01 | 87.7% | 67.3% |
| 4536448 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.67 | 32.0 | 3.48e-01 | 85.6% | 54.2% |
| 4964957 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.65 | 31.0 | 3.43e-01 | 84.2% | 55.7% |
| 4974007 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.65 | 31.0 | 3.40e-01 | 84.9% | 53.3% |
| 3386395 | 2484.1.1.178 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA+FtsA | 0.65 | 34.0 | 3.26e-01 | 84.9% | 44.1% |
| 4282149 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.64 | 31.0 | 3.43e-01 | 85.6% | 55.0% |
| 3911145 | 223.7.1.1 ↗ | a+b three layers › Profilin-like › FLJ32549 C-terminal domain-like › FLJ32549 C-terminal domain-like › C12orf66_like | 0.64 | 33.0 | 3.44e-01 | 95.2% | 51.4% |
| 4464341 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.64 | 33.0 | 3.67e-01 | 84.9% | 60.8% |
| 4264673 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.63 | 33.0 | 3.60e-01 | 84.9% | 60.0% |
| 3790377 | 223.2.1.49 ↗ | a+b three layers › Profilin-like › profilin-like › profilin-like › C12orf66_like | 0.62 | 33.0 | 3.35e-01 | 95.2% | 49.3% |
| 4982365 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.62 | 31.0 | 3.31e-01 | 85.6% | 53.6% |
| 5070445 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.62 | 31.0 | 3.43e-01 | 84.9% | 57.5% |
| 4159425 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.62 | 31.0 | 3.43e-01 | 85.6% | 57.5% |
| 4425543 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.62 | 31.0 | 3.31e-01 | 85.6% | 54.4% |
| 4992358 | 274.1.1.0 ↗ | a+b two layers › Pili subunits › Pili subunits › Pili subunits | 0.61 | 31.0 | 3.29e-01 | 82.2% | 53.3% |
| 4983075 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.61 | 32.0 | 3.48e-01 | 84.9% | 58.4% |
| 5012088 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.61 | 30.0 | 3.46e-01 | 84.9% | 61.8% |
| 4093975 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.61 | 31.0 | 3.46e-01 | 84.9% | 60.0% |
| 4937734 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.60 | 30.0 | 3.36e-01 | 84.2% | 59.1% |
| 3700519 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.60 | 32.0 | 3.31e-01 | 84.9% | 51.7% |
| 4497431 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.60 | 32.0 | 3.41e-01 | 84.9% | 58.4% |
| 4991620 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.60 | 32.0 | 3.58e-01 | 85.6% | 64.3% |
| 4230630 | 2484.1.1.11 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_L18p | 0.59 | 35.0 | 3.87e-01 | 92.5% | 72.6% |
| 4634374 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.59 | 31.0 | 3.44e-01 | 84.9% | 60.8% |
| 3276788 | 376.1.1.0 ↗ | few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box | 0.59 | 34.0 | 3.69e-01 | 89.0% | 65.6% |
| 5031007 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.59 | 31.0 | 3.38e-01 | 85.6% | 58.4% |
| 5081896 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.59 | 30.0 | 3.23e-01 | 84.9% | 55.4% |
| 4969626 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.59 | 30.0 | 3.21e-01 | 84.9% | 55.2% |
| 3987555 | 2484.1.1.27 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA | 0.59 | 33.0 | 2.93e-01 | 88.4% | 38.0% |
| 4190296 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.58 | 31.0 | 3.40e-01 | 84.9% | 60.8% |
| 134040 | 4312.1.1.3 ↗ | a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin | 0.58 | 32.0 | 3.90e-01 | 87.7% | 83.2% |
| 3984362 | 1.1.9.32 ↗ | beta barrels › cradle loop barrel › RIFT-related › PUA domain › TnpB_IS66 | 0.58 | 33.0 | 4.00e-01 | 82.2% | 86.3% |
| 4656410 | 1.1.9.32 ↗ | beta barrels › cradle loop barrel › RIFT-related › PUA domain › TnpB_IS66 | 0.57 | 33.0 | 4.04e-01 | 81.5% | 91.0% |
| 5075835 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.57 | 31.0 | 3.29e-01 | 84.9% | 56.9% |
| 5041103 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.57 | 29.0 | 3.21e-01 | 84.9% | 57.5% |
| 5058725 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.57 | 29.0 | 3.15e-01 | 84.9% | 56.8% |
| 2814146 | 896.1.1.1 ↗ | a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Ribosomal_L38e | 0.57 | 28.0 | 3.81e-01 | 98.6% | 90.8% |
| 4254268 | 2484.4.1.1 ↗ | mixed a+b and a/b › Ribonuclease H-like › Nitrogenase accessory factor-like › Nitrogenase accessory factor-like › Nitro_FeMo-Co | 0.57 | 31.0 | 3.38e-01 | 85.6% | 63.3% |
| 5000524 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.57 | 31.0 | 3.32e-01 | 85.6% | 59.2% |
| 5035283 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.56 | 30.0 | 3.27e-01 | 84.9% | 58.4% |
| 5033346 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.56 | 29.0 | 3.12e-01 | 84.9% | 56.0% |
| 4937453 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.54 | 32.0 | 3.39e-01 | 84.9% | 63.7% |
| 5033640 | 2.1.1.15 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon | 0.53 | 29.0 | 3.23e-01 | 89.7% | 67.3% |
| 4939492 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.53 | 28.0 | 2.96e-01 | 84.9% | 54.4% |
| 3674329 | 2484.1.1.11 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_L18p | 0.52 | 34.0 | 3.59e-01 | 92.5% | 71.9% |
| 3207467 | 2484.1.1.38 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 | 0.52 | 32.0 | 3.17e-01 | 84.9% | 57.4% |
| 3982093 | 268.1.1.1 ↗ | a+b two layers › Sterol carrier protein-like › Sterol carrier protein, SCP-related › Sterol carrier protein, SCP-related › SCP2 | 0.52 | 39.0 | 4.00e-01 | 98.6% | 81.4% |
| 4963804 | 2484.1.1.339 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › acVLRF1 | 0.51 | 32.0 | 3.35e-01 | 85.6% | 67.9% |