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SRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00178
Bact-VirSRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00178
Identity
- Kingdom:
- phage
Quality
76.6
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 151-262
Domain cluster:
representative
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2l6lA02 | 3.10.660.10 | Alpha Beta › Roll › Microbial ribonuclease fold › DPH Zinc finger | 0.58 | 23.0 | 2.85e-01 | 73.2% | 55.4% |
| 1s58A00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.51 | 43.0 | 2.86e-01 | 97.3% | 80.9% |
D2
high
residues 463-610
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03734.20 best | YkuD | 53.4 | 5.90e-14 | 99.3% | 97.3% |
CATH (7)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1zatA02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.95 | 75.0 | 8.30e-01 | 100.0% | 97.6% |
| 3tx4A02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.91 | 75.0 | 7.65e-01 | 100.0% | 87.3% |
| 2mtzA02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.85 | 60.0 | 6.70e-01 | 100.0% | 89.1% |
| 4z7aA03 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.85 | 64.0 | 6.83e-01 | 100.0% | 87.0% |
| 4lpqA02 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.83 | 66.0 | 7.05e-01 | 100.0% | 93.0% |
| 6xj6A01 | 2.40.440.10 | Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like | 0.69 | 59.0 | 5.84e-01 | 100.0% | 84.6% |
| 5ldyA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.50 | 31.0 | 3.54e-01 | 100.0% | 84.0% |
ECOD (24)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1558018 | 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 | 0.94 | 68.0 | 7.35e-01 | 100.0% | 84.6% |
| 3957156 | 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 | 0.94 | 66.0 | 7.09e-01 | 100.0% | 81.5% |
| 3968640 | 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 | 0.93 | 67.0 | 7.34e-01 | 100.0% | 87.2% |
| 3283151 | 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 | 0.93 | 65.0 | 7.67e-01 | 100.0% | 97.2% |
| 1220824 | 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 | 0.91 | 75.0 | 6.97e-01 | 100.0% | 71.3% |
| 3960486 | 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 | 0.91 | 72.0 | 7.20e-01 | 100.0% | 80.0% |
| 997880 | 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 | 0.89 | 71.0 | 7.64e-01 | 100.0% | 94.6% |
| 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 | 63.0 | 6.39e-01 | 100.0% | 76.6% |
| 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 | 0.84 | 72.0 | 6.33e-01 | 100.0% | 64.5% |
| 1120883 | 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 | 0.83 | 66.0 | 7.05e-01 | 100.0% | 93.0% |
| 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 | 0.83 | 68.0 | 7.31e-01 | 100.0% | 96.9% |
| 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 | 0.83 | 67.0 | 6.96e-01 | 100.0% | 89.1% |
| 4679621 | 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 | 0.82 | 69.0 | 7.33e-01 | 100.0% | 96.3% |
| 3981189 | 3743.1.1.0 ↗ | a+b two layers › L,D-transpeptidase C-terminal domain › L,D-transpeptidase C-terminal domain › L,D-transpeptidase C-terminal domain | 0.80 | 70.0 | 5.94e-01 | 100.0% | 59.6% |
| None | — | 0.80 | 70.0 | 7.02e-01 | 100.0% | 89.3% | |
| 3951628 | 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 | 0.79 | 74.0 | 7.39e-01 | 100.0% | 94.7% |
| 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 | 0.79 | 69.0 | 7.04e-01 | 100.0% | 92.4% |
| 3958193 | 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 | 0.74 | 68.0 | 6.77e-01 | 98.6% | 92.7% |
| 3163824 | 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 | 0.73 | 70.0 | 5.52e-01 | 100.0% | 70.9% |
| 2819641 | 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 | 0.73 | 69.0 | 5.86e-01 | 100.0% | 85.5% |
| 3969743 | 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 | 0.72 | 63.0 | 6.56e-01 | 100.0% | 96.4% |
| 3971742 | 4091.1.1.2 ↗ | beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD_2 | 0.67 | 61.0 | 5.40e-01 | 100.0% | 69.5% |
| 4056773 | 325.1.7.3 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Apocytochr_F_C | 0.55 | 30.0 | 3.74e-01 | 83.1% | 90.6% |
| 3490327 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.51 | 25.0 | 2.72e-01 | 79.7% | 53.1% |
D3
medium
residues 263-285_320-401_417-449
Domain cluster:
representative
CATH (4)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1zatA01 | 3.10.20.800 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.81 | 60.0 | 6.33e-01 | 76.1% | 98.4% |
| 4bwxA03 | 1.10.287.3700 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.58 | 21.0 | 2.74e-01 | 84.8% | 55.0% |
| 1tzlA02 | 3.30.1920.50 | Alpha Beta › 2-Layer Sandwich › Phage tail proteins - 2 layer sandwich fold › | 0.56 | 23.0 | 3.35e-01 | 86.2% | 82.3% |
| 1wx8A00 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.51 | 30.0 | 3.42e-01 | 71.7% | 79.2% |
ECOD (5)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2445413 | 4228.1.1.1 ↗ | a+b complex topology › L,D-transpeptidase pre-catalytic domain-like › L,D-transpeptidase pre-catalytic domain-like › L,D-transpeptidase pre-catalytic domain-like › PG_binding_4 | 0.80 | 61.0 | 6.39e-01 | 78.3% | 96.8% |
| 3588724 | 4228.1.1.1 ↗ | a+b complex topology › L,D-transpeptidase pre-catalytic domain-like › L,D-transpeptidase pre-catalytic domain-like › L,D-transpeptidase pre-catalytic domain-like › PG_binding_4 | 0.79 | 74.0 | 6.07e-01 | 100.0% | 75.8% |
| 3170703 | 376.1.1.129 ↗ | few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › PF29536 | 0.54 | 32.0 | 3.51e-01 | 81.2% | 72.7% |
| 4406321 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.53 | 20.0 | 2.72e-01 | 81.2% | 62.9% |
| 3799216 | 5067.1.1.0 ↗ | alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain | 0.53 | 46.0 | 2.87e-01 | 94.9% | 89.1% |