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NC_070859.1__YP_010658648.1__PP753_gp75__00044
Bact-VirNC_070859.1__YP_010658648.1__PP753_gp75__00044
Identity
- Accession:
- NC_070859 ↗
- Kingdom:
- phage
Quality
87.7
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Schitoviridae›
Gonggongvirus›
Dinoroseobacter_phage_vB_DshP-R7L
TaxID: 2873349
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 30-209
Domain cluster:
rep: IMGVR_UViG_3300039190_000305-3300039190-Ga0399989_003201_3_1937__D82-97_167-336
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF13589.13 best | HATPase_c_3 | 25.8 | 1.40e-05 | 66.7% | 72.3% |
D2
high
residues 223-303
Domain cluster:
rep: MW824370.1__QZI89871.1__MYOV002v2_p0166__00166__D290-363
CATH (9)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1b63A02 | 3.30.230.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › | 0.62 | 54.0 | 4.87e-01 | 100.0% | 78.9% |
| 2gs8A01 | 3.30.230.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › | 0.60 | 49.0 | 3.82e-01 | 100.0% | 40.9% |
| 1y6zA01 | 3.30.230.80 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › | 0.59 | 45.0 | 3.68e-01 | 100.0% | 42.9% |
| 1t3uA01 | 3.30.160.880 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Cell division protein ZapA protomer, N-terminal domain | 0.57 | 24.0 | 3.26e-01 | 72.8% | 74.4% |
| 3ltoA01 | 3.30.230.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › | 0.52 | 46.0 | 3.62e-01 | 100.0% | 68.3% |
| 3ic6A01 | 3.40.1280.10 | Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain | 0.52 | 38.0 | 2.88e-01 | 77.8% | 87.9% |
| 2ppiA01 | 3.30.710.10 | Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A | 0.52 | 40.0 | 3.67e-01 | 85.2% | 71.3% |
| 4p52A01 | 3.30.230.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › | 0.51 | 44.0 | 3.49e-01 | 100.0% | 61.1% |
| 3hqiA02 | 3.30.710.10 | Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A | 0.51 | 39.0 | 3.33e-01 | 85.2% | 53.6% |
ECOD (21)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3823703 | 212.1.1.22 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Topo-VIb_trans | 0.67 | 59.0 | 4.27e-01 | 100.0% | 54.2% |
| 3246869 | 212.1.1.0 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like | 0.66 | 57.0 | 4.16e-01 | 100.0% | 33.3% |
| 3487862 | 212.1.1.0 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like | 0.66 | 57.0 | 4.14e-01 | 100.0% | 33.3% |
| 3869716 | 212.1.1.24 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Morc6_S5 | 0.66 | 57.0 | 4.71e-01 | 100.0% | 53.3% |
| 3968852 | 212.1.1.1 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › HSP90 | 0.66 | 59.0 | 4.80e-01 | 100.0% | 82.7% |
| 2323907 | 212.1.1.24 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Morc6_S5 | 0.65 | 57.0 | 4.19e-01 | 100.0% | 35.7% |
| 3615913 | 212.1.1.9 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › DNA_mis_repair | 0.63 | 55.0 | 4.78e-01 | 100.0% | 73.8% |
| 3470861 | 212.1.1.9 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › DNA_mis_repair | 0.62 | 54.0 | 4.57e-01 | 100.0% | 67.1% |
| 1207703 | 212.1.1.9 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › DNA_mis_repair | 0.58 | 50.0 | 4.39e-01 | 100.0% | 71.1% |
| 3929070 | 226.1.1.0 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain | 0.58 | 46.0 | 4.08e-01 | 87.7% | 66.7% |
| 3619868 | 226.1.1.1 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain › BTB | 0.57 | 44.0 | 4.00e-01 | 82.7% | 70.9% |
| 4094315 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.56 | 44.0 | 3.59e-01 | 100.0% | 43.8% |
| 3412904 | 226.1.1.1 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain › BTB | 0.56 | 43.0 | 3.71e-01 | 82.7% | 63.1% |
| 4927937 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.56 | 47.0 | 3.23e-01 | 100.0% | 25.6% |
| 4522268 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.55 | 45.0 | 3.52e-01 | 100.0% | 40.0% |
| 3988608 | 212.1.1.25 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › MVD-like_N | 0.55 | 48.0 | 3.82e-01 | 100.0% | 65.3% |
| 3223584 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.55 | 48.0 | 3.57e-01 | 100.0% | 42.3% |
| 4529995 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.55 | 45.0 | 3.72e-01 | 100.0% | 48.1% |
| 4234779 | 212.1.1.3 ↗ | a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › GHMP_kinases_N | 0.54 | 41.0 | 3.34e-01 | 100.0% | 40.6% |
| 3216229 | 226.1.1.1 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain › BTB | 0.54 | 42.0 | 3.53e-01 | 85.2% | 56.4% |
| 3568729 | 226.1.1.1 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain › BTB | 0.52 | 40.0 | 3.63e-01 | 85.2% | 67.8% |
D3
high
residues 311-423
Domain cluster:
rep: MH015250.1__AWY08830.1__vBRpoPV12_43__00043__D135-240
D4
high
residues 434-543_580-608
Domain cluster:
representative
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4fh3A02 | 3.30.460.10 | Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 | 0.63 | 39.0 | 4.14e-01 | 100.0% | 68.8% |
| 3tvzB00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 27.0 | 2.77e-01 | 100.0% | 41.6% |
| 1m55A00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.54 | 37.0 | 3.28e-01 | 100.0% | 49.7% |
| 3daoA02 | 3.30.1240.10 | Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › | 0.53 | 36.0 | 4.06e-01 | 96.4% | 89.0% |
| 1v4pC01 | 3.30.980.10 | Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 | 0.52 | 33.0 | 3.73e-01 | 100.0% | 82.4% |
| 2hfqA00 | 3.10.510.10 | Alpha Beta › Roll › NE1680-like fold › NE1680-like | 0.52 | 23.0 | 2.94e-01 | 72.7% | 69.4% |
ECOD (11)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5005787 | 327.7.1.2 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › FKBP26_C | 0.65 | 31.0 | 4.31e-01 | 91.4% | 95.4% |
| 3972149 | 322.1.1.1 ↗ | a+b two layers › HPr-like › HPr-like › HPr-like › PTS-HPr | 0.62 | 34.0 | 4.23e-01 | 95.7% | 90.0% |
| 5035854 | 329.1.1.2 ↗ | a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 | 0.61 | 38.0 | 4.19e-01 | 92.8% | 77.3% |
| 3790774 | 223.1.1.0 ↗ | a+b three layers › Profilin-like › sensor domains › sensor domains | 0.59 | 40.0 | 4.33e-01 | 97.1% | 81.7% |
| 5060151 | 329.1.1.2 ↗ | a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 | 0.58 | 36.0 | 4.15e-01 | 92.8% | 86.0% |
| 4929138 | 329.1.1.2 ↗ | a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 | 0.58 | 36.0 | 4.02e-01 | 94.2% | 79.1% |
| 5077294 | 329.1.1.2 ↗ | a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 | 0.57 | 35.0 | 3.98e-01 | 94.2% | 84.0% |
| 3981506 | 301.3.1.1 ↗ | a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA | 0.56 | 31.0 | 2.95e-01 | 97.1% | 46.9% |
| 3476713 | 601.23.1.4 ↗ | alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III | 0.53 | 32.0 | 2.37e-01 | 99.3% | 24.5% |
| 5049882 | 329.1.1.2 ↗ | a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 | 0.53 | 36.0 | 3.82e-01 | 92.1% | 79.0% |
| 5469 | 4943.1.1.2 ↗ | a+b two layers › YcgL/NE1680-like › YcgL/NE1680-like › YcgL/NE1680-like › DUF2024 | 0.52 | 23.0 | 2.94e-01 | 72.7% | 69.4% |
D5
high
residues 636-701
Domain cluster:
representative
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4atyA00 | 3.40.718.10 | Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase | 0.60 | 41.0 | 2.67e-01 | 71.2% | 23.0% |
| 6ziwI02 | 1.10.510.10 | Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 | 0.55 | 41.0 | 3.11e-01 | 83.3% | 90.1% |
| 3d3kA00 | 3.40.50.10260 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › YjeF N-terminal domain | 0.54 | 37.0 | 2.59e-01 | 71.2% | 44.6% |
| 5tvwA01 | 3.40.50.11260 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.54 | 46.0 | 3.92e-01 | 100.0% | 56.9% |
| 2mhcA00 | 3.40.50.1390 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Resolvase, N-terminal catalytic domain | 0.54 | 37.0 | 3.09e-01 | 72.7% | 53.3% |
| 1ao8A00 | 3.40.430.10 | Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A | 0.50 | 34.0 | 2.64e-01 | 71.2% | 81.5% |
ECOD (10)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3942893 | 3012.1.1.0 ↗ | a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain | 0.68 | 38.0 | 3.28e-01 | 72.7% | 35.0% |
| 4982675 | 2007.1.5.2 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › CCG | 0.59 | 47.0 | 3.81e-01 | 92.4% | 59.3% |
| 4261213 | 2005.1.1.1 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 | 0.59 | 40.0 | 2.53e-01 | 71.2% | 89.7% |
| 1518790 | 2485.1.1.41 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_4 | 0.59 | 43.0 | 4.27e-01 | 92.4% | 75.4% |
| 3728663 | 2003.1.1.53 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NmrA | 0.57 | 39.0 | 2.52e-01 | 71.2% | 31.5% |
| 4933780 | 2007.1.5.2 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › CCG | 0.56 | 44.0 | 3.48e-01 | 90.9% | 51.9% |
| 4030453 | 140.1.1.0 ↗ | alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.55 | 40.0 | 2.36e-01 | 81.8% | 45.3% |
| 4541761 | 2005.1.1.29 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1g | 0.55 | 38.0 | 2.60e-01 | 77.3% | 77.4% |
| 4512470 | 2005.1.1.1 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 | 0.53 | 42.0 | 2.62e-01 | 90.9% | 82.6% |
| 5028148 | 7514.1.1.1 ↗ | a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_1 | 0.52 | 35.0 | 2.92e-01 | 71.2% | 70.8% |
D6
high
residues 717-854
Domain cluster:
rep: MH015250.1__AWY08831.1__vBRpoPV12_44__00044__D136-271