←Back to structures
NC_024787.1__YP_009055704.1__LD12_gp128__00116
Bact-VirNC_024787.1__YP_009055704.1__LD12_gp128__00116
Identity
- Accession:
- NC_024787 ↗
- Kingdom:
- phage
Quality
78.3
mean pLDDT
Taxonomy
TaxID: 1486413
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 10-68
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF09636.17 best | XkdW | 37.2 | 2.90e-09 | 94.9% | 91.2% |
CATH (28)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2hg7A00 | 3.30.56.60 | Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › XkdW-like | 0.81 | 71.0 | 7.13e-01 | 100.0% | 95.0% |
| 3dluA00 | 3.30.56.30 | Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › Signal recognition particle, SRP19-like subunit | 0.63 | 54.0 | 4.66e-01 | 100.0% | 62.1% |
| 2felA00 | 1.20.200.10 | Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) | 0.59 | 49.0 | 3.15e-01 | 98.3% | 57.3% |
| 2j3tC00 | 3.30.450.70 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › | 0.59 | 40.0 | 3.04e-01 | 71.2% | 34.0% |
| 2m89A00 | 3.30.530.20 | Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain | 0.58 | 45.0 | 3.60e-01 | 89.8% | 88.8% |
| 2rhqB06 | 3.30.70.380 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain | 0.58 | 45.0 | 4.14e-01 | 89.8% | 78.3% |
| 3jcmH04 | 3.30.70.870 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 | 0.58 | 42.0 | 3.89e-01 | 91.5% | 61.0% |
| 1x9mA03 | 3.30.70.370 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 48.0 | 3.52e-01 | 98.3% | 34.8% |
| 2cxiA03 | 3.30.56.10 | Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › | 0.56 | 41.0 | 4.00e-01 | 100.0% | 70.0% |
| 2dr1A01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.55 | 45.0 | 3.55e-01 | 94.9% | 42.2% |
| 3encA00 | 3.30.310.50 | Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain | 0.55 | 43.0 | 3.97e-01 | 89.8% | 68.4% |
| 4nkpA01 | 3.30.450.150 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem-degrading domain | 0.55 | 42.0 | 3.42e-01 | 89.8% | 95.4% |
| 2qsrA01 | 3.90.1150.50 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription-repair-coupling factor, D7 domain | 0.55 | 44.0 | 3.36e-01 | 96.6% | 35.5% |
| 7k98E03 | 3.30.56.10 | Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › | 0.54 | 46.0 | 4.45e-01 | 100.0% | 94.1% |
| 1szsA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.54 | 41.0 | 3.09e-01 | 86.4% | 53.9% |
| 2fyiC01 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.54 | 39.0 | 3.10e-01 | 78.0% | 66.9% |
| 4mt1A07 | 3.30.70.1440 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain | 0.53 | 41.0 | 3.56e-01 | 89.8% | 56.9% |
| 6wngA02 | 1.20.200.10 | Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) | 0.53 | 46.0 | 3.00e-01 | 100.0% | 82.7% |
| 5i9eA03 | 3.90.640.10 | Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 | 0.53 | 43.0 | 3.65e-01 | 98.3% | 99.1% |
| 4ga6A04 | 3.90.1170.30 | Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Pyrimidine nucleoside phosphorylase-like, C-terminal domain | 0.53 | 39.0 | 3.71e-01 | 88.1% | 76.5% |
| 4pv6A00 | 3.40.630.30 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) | 0.53 | 36.0 | 2.79e-01 | 74.6% | 42.9% |
| 1u9tA02 | 3.40.1570.10 | Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains | 0.52 | 37.0 | 2.77e-01 | 78.0% | 53.8% |
| 4ebrA00 | 3.30.1460.50 | Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › | 0.51 | 40.0 | 3.04e-01 | 89.8% | 38.2% |
| 7xinA03 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.51 | 38.0 | 3.32e-01 | 89.8% | 48.6% |
| 1kvnA00 | 3.30.56.30 | Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › Signal recognition particle, SRP19-like subunit | 0.51 | 41.0 | 3.63e-01 | 100.0% | 84.6% |
| 1jb7A01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.51 | 41.0 | 2.96e-01 | 88.1% | 83.9% |
| 3fpwA01 | 3.30.450.150 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem-degrading domain | 0.50 | 41.0 | 3.27e-01 | 91.5% | 93.6% |
| 3f0zA02 | 1.10.340.30 | Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 | 0.50 | 41.0 | 3.41e-01 | 100.0% | 98.3% |
ECOD (51)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4567341 | 4989.1.1.1 ↗ | a+b two layers › XkdW-like › XkdW-like › XkdW-like › XkdW | 0.83 | 74.0 | 7.44e-01 | 100.0% | 96.7% |
| 4945 | 4989.1.1.1 ↗ | a+b two layers › XkdW-like › XkdW-like › XkdW-like › XkdW | 0.81 | 71.0 | 7.13e-01 | 100.0% | 95.0% |
| 3800293 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.62 | 48.0 | 4.28e-01 | 89.8% | 63.4% |
| 4936622 | 305.1.1.1 ↗ | a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L | 0.62 | 51.0 | 4.52e-01 | 100.0% | 63.2% |
| 4668421 | 304.162.1.1 ↗ | a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH | 0.60 | 46.0 | 4.21e-01 | 84.7% | 75.0% |
| 4679312 | 304.162.1.1 ↗ | a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH | 0.59 | 45.0 | 4.13e-01 | 84.7% | 75.0% |
| 3247481 | 327.5.1.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins | 0.59 | 45.0 | 4.57e-01 | 94.9% | 88.3% |
| 5052421 | 305.1.1.2 ↗ | a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L_2 | 0.59 | 49.0 | 4.33e-01 | 100.0% | 62.1% |
| 3955130 | 304.48.1.48 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF_2 | 0.59 | 46.0 | 3.55e-01 | 94.9% | 34.5% |
| 3459288 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.59 | 44.0 | 4.17e-01 | 84.7% | 72.0% |
| 4411246 | 304.162.1.1 ↗ | a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH | 0.58 | 43.0 | 4.02e-01 | 84.7% | 75.0% |
| 3615029 | 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 | 0.58 | 48.0 | 4.22e-01 | 94.9% | 66.7% |
| 5041064 | 305.2.1.1 ↗ | a+b two layers › DCoH-like › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin_4a | 0.58 | 45.0 | 3.95e-01 | 89.8% | 62.1% |
| 3645785 | 304.8.1.57 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_ACR_D1 | 0.58 | 45.0 | 3.85e-01 | 89.8% | 53.3% |
| 4928996 | 2004.1.1.173 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind | 0.57 | 48.0 | 2.98e-01 | 100.0% | 42.1% |
| 3413123 | 3343.1.1.1 ↗ | alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal | 0.57 | 42.0 | 2.44e-01 | 84.7% | 16.7% |
| 3439107 | 304.8.1.45 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant | 0.57 | 44.0 | 4.14e-01 | 89.8% | 85.3% |
| 1117622 | 330.1.1.7 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsRBD2 | 0.57 | 40.0 | 3.42e-01 | 94.9% | 44.6% |
| 3911603 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.56 | 40.0 | 2.97e-01 | 89.8% | 27.9% |
| 3180719 | 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 | 0.55 | 43.0 | 3.77e-01 | 91.5% | 54.1% |
| 4679172 | 331.2.1.1 ↗ | a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM_PMM_IV | 0.55 | 41.0 | 3.77e-01 | 83.1% | 71.2% |
| 3733471 | 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 | 0.55 | 45.0 | 3.89e-01 | 94.9% | 59.0% |
| 3881654 | 2484.1.1.2 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin | 0.54 | 46.0 | 3.10e-01 | 98.3% | 49.4% |
| 4945248 | 325.1.3.0 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain | 0.54 | 40.0 | 3.58e-01 | 84.7% | 65.3% |
| 3302370 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.54 | 43.0 | 3.98e-01 | 94.9% | 75.9% |
| 3744259 | 101.1.2.154 ↗ | alpha arrays › HTH › HTH › winged helix domain › CDT1_C | 0.54 | 42.0 | 3.27e-01 | 100.0% | 38.5% |
| 3597807 | 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 | 0.54 | 44.0 | 3.55e-01 | 96.6% | 44.6% |
| 4289835 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.54 | 45.0 | 3.12e-01 | 94.9% | 54.3% |
| 4548733 | 325.1.3.1 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain › PYNP_C | 0.54 | 39.0 | 3.49e-01 | 83.1% | 69.5% |
| 5060221 | 325.1.3.1 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain › PYNP_C | 0.53 | 40.0 | 3.79e-01 | 88.1% | 77.5% |
| 3367471 | 304.8.1.45 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant | 0.53 | 41.0 | 3.96e-01 | 89.8% | 84.3% |
| 4312637 | 325.1.3.1 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain › PYNP_C | 0.53 | 42.0 | 3.68e-01 | 89.8% | 64.2% |
| 4309865 | 325.1.3.0 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain | 0.53 | 40.0 | 3.76e-01 | 88.1% | 78.8% |
| 5036327 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.53 | 41.0 | 4.02e-01 | 89.8% | 86.2% |
| 3617823 | 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 | 0.53 | 44.0 | 3.90e-01 | 100.0% | 71.0% |
| 4545327 | 325.1.3.1 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain › PYNP_C | 0.53 | 39.0 | 3.50e-01 | 84.7% | 64.2% |
| 3837690 | 304.8.1.2 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT | 0.53 | 40.0 | 3.80e-01 | 88.1% | 81.3% |
| 4536447 | 325.1.3.1 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Pyrimidine nucleoside phosphorylase C-terminal domain › PYNP_C | 0.53 | 40.0 | 3.61e-01 | 89.8% | 66.3% |
| 3807910 | 304.8.1.45 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant | 0.53 | 41.0 | 3.89e-01 | 94.9% | 76.2% |
| 3700873 | 3343.1.1.2 ↗ | alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal | 0.53 | 41.0 | 2.39e-01 | 89.8% | 13.9% |
| 3425342 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.53 | 41.0 | 3.94e-01 | 94.9% | 85.3% |
| 3545474 | 327.11.2.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) | 0.52 | 42.0 | 3.83e-01 | 98.3% | 82.2% |
| 4950083 | 223.2.1.0 ↗ | a+b three layers › Profilin-like › profilin-like › profilin-like | 0.52 | 41.0 | 3.52e-01 | 89.8% | 78.6% |
| 3699689 | 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 | 0.52 | 42.0 | 3.87e-01 | 96.6% | 67.1% |
| 4991988 | 3501.1.1.1 ↗ | a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 › Pcc1 | 0.52 | 42.0 | 4.02e-01 | 94.9% | 80.0% |
| 3258201 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.51 | 42.0 | 2.96e-01 | 100.0% | 72.8% |
| 4995220 | 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 | 39.0 | 3.44e-01 | 89.8% | 57.0% |
| 3931290 | 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 | 41.0 | 3.45e-01 | 100.0% | 54.2% |
| 3253944 | 5041.1.1.0 ↗ | extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C | 0.51 | 36.0 | 2.64e-01 | 96.6% | 25.7% |
| 4480786 | 304.28.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran | 0.51 | 40.0 | 3.51e-01 | 94.9% | 67.0% |
| 3932018 | 168.1.1.0 ↗ | alpha arrays › Sec7 domain › Sec7 domain › Sec7 domain | 0.51 | 37.0 | 2.11e-01 | 84.7% | 9.9% |