←Back to structures
LSDeep1_scaffold_42_prodigal-single.1__X__X__00041
Bact-VirLSDeep1_scaffold_42_prodigal-single.1__X__X__00041
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 4-77
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01541.31 best | GIY-YIG | 38.1 | 2.20e-09 | 100.0% | 85.9% |
CATH (34)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1ln0A00 | 3.40.1440.10 | Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.90 | 84.0 | 7.73e-01 | 100.0% | 84.8% |
| 4dohE02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.76 | 47.0 | 4.11e-01 | 86.5% | 43.4% |
| 1wgrA01 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.73 | 41.0 | 4.00e-01 | 75.7% | 50.0% |
| 2ww8A01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.71 | 43.0 | 3.79e-01 | 81.1% | 42.5% |
| 3h20A01 | 3.30.1490.240 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain | 0.68 | 45.0 | 4.72e-01 | 82.4% | 75.8% |
| 2aehA01 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.67 | 43.0 | 3.97e-01 | 91.9% | 50.0% |
| 4pofA03 | 2.20.28.10 | Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › | 0.67 | 43.0 | 5.06e-01 | 79.7% | 98.0% |
| 1ltlA03 | 2.20.28.10 | Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › | 0.64 | 41.0 | 4.79e-01 | 79.7% | 98.0% |
| 4me3A03 | 2.20.28.10 | Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › | 0.62 | 44.0 | 4.86e-01 | 79.7% | 100.0% |
| 1qysA00 | 3.30.1710.10 | Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein | 0.59 | 41.0 | 3.81e-01 | 78.4% | 57.6% |
| 3rp6A02 | 3.30.9.30 | Alpha Beta › 2-Layer Sandwich › D-Amino Acid Oxidase; Chain A, domain 2 › | 0.59 | 52.0 | 3.75e-01 | 100.0% | 51.6% |
| 4kyzA00 | 3.30.70.600 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 | 0.58 | 39.0 | 3.08e-01 | 78.4% | 31.7% |
| 2jvfA00 | 3.30.1710.10 | Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein | 0.57 | 39.0 | 3.62e-01 | 78.4% | 56.4% |
| 7ejoB01 | 3.30.2260.10 | Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary | 0.56 | 42.0 | 4.04e-01 | 79.7% | 75.9% |
| 3in6A02 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 45.0 | 3.87e-01 | 87.8% | 79.5% |
| 2gffA00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.56 | 44.0 | 4.08e-01 | 86.5% | 100.0% |
| 3am2A02 | 2.60.120.1050 | Mainly Beta › Sandwich › Jelly Rolls › | 0.55 | 35.0 | 3.08e-01 | 81.1% | 41.0% |
| 5kycB02 | 2.20.210.10 | Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › ubp-family deubiquitinating enzyme superfamily | 0.55 | 37.0 | 4.18e-01 | 81.1% | 98.1% |
| 4iyqA00 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.54 | 43.0 | 3.93e-01 | 90.5% | 91.6% |
| 2bbhA01 | 3.30.460.20 | Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like | 0.54 | 32.0 | 2.61e-01 | 81.1% | 27.8% |
| 3ir9A02 | 3.30.1330.30 | Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 | 0.54 | 43.0 | 3.67e-01 | 86.5% | 67.5% |
| 1wkyA02 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.54 | 37.0 | 3.03e-01 | 86.5% | 36.8% |
| 1ca1A02 | 2.60.60.20 | Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain | 0.53 | 38.0 | 3.32e-01 | 77.0% | 80.0% |
| 3tcaA01 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.53 | 41.0 | 3.87e-01 | 98.6% | 67.8% |
| 4m0wA03 | 2.60.120.1680 | Mainly Beta › Sandwich › Jelly Rolls › | 0.53 | 39.0 | 3.25e-01 | 82.4% | 43.1% |
| 7rlrA01 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.53 | 38.0 | 2.77e-01 | 78.4% | 66.3% |
| 2iq1A00 | 3.60.40.10 | Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain | 0.53 | 39.0 | 2.76e-01 | 81.1% | 30.0% |
| 4uuwA03 | 3.90.950.20 | Alpha Beta › Alpha-Beta Complex › Maf protein › CinA-like | 0.52 | 38.0 | 3.14e-01 | 78.4% | 84.4% |
| 7ylrA01 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.52 | 37.0 | 3.36e-01 | 75.7% | 69.5% |
| 4iajA00 | 3.30.1490.390 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 | 0.52 | 34.0 | 3.40e-01 | 78.4% | 64.5% |
| 2zt5A02 | 3.30.40.230 | Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › | 0.52 | 43.0 | 4.15e-01 | 91.9% | 100.0% |
| 2x3gA00 | 3.30.70.1910 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.52 | 45.0 | 3.91e-01 | 100.0% | 79.3% |
| 4ekuA01 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.51 | 37.0 | 3.27e-01 | 77.0% | 75.2% |
| 1l1lA01 | 3.20.70.20 | Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › | 0.51 | 39.0 | 2.43e-01 | 86.5% | 68.7% |
ECOD (46)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4344289 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.91 | 85.0 | 6.89e-01 | 100.0% | 63.1% |
| 4677975 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.90 | 84.0 | 7.04e-01 | 100.0% | 67.8% |
| 4397568 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.86 | 72.0 | 6.68e-01 | 100.0% | 73.3% |
| 3215217 | 821.1.1.7 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › LEM-3_GIY-YIG | 0.78 | 71.0 | 5.43e-01 | 100.0% | 55.8% |
| 3467170 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.78 | 60.0 | 6.40e-01 | 86.5% | 95.2% |
| 4945828 | 821.1.1.0 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.76 | 65.0 | 6.13e-01 | 100.0% | 77.8% |
| 4981567 | 821.1.1.0 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.74 | 67.0 | 5.60e-01 | 100.0% | 67.2% |
| 4995774 | 375.1.1.185 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_8 | 0.71 | 40.0 | 5.02e-01 | 73.0% | 100.0% |
| 3620613 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.70 | 42.0 | 5.11e-01 | 77.0% | 100.0% |
| 3551231 | 221.1.1.87 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 | 0.69 | 44.0 | 3.92e-01 | 91.9% | 45.7% |
| 1176816 | 244.1.1.0 ↗ | a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C | 0.67 | 49.0 | 4.43e-01 | 78.4% | 92.3% |
| 5016960 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.67 | 40.0 | 4.91e-01 | 75.7% | 100.0% |
| 5026915 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.66 | 43.0 | 4.97e-01 | 79.7% | 98.0% |
| 4970537 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.66 | 36.0 | 4.52e-01 | 75.7% | 97.5% |
| 3738005 | 3868.1.1.1 ↗ | a+b three layers › Mitochondrial homologous recombination protein 1 › Mitochondrial homologous recombination protein 1 › Mitochondrial homologous recombination protein 1 › Mhr1 | 0.66 | 60.0 | 4.66e-01 | 100.0% | 49.7% |
| 4929321 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.65 | 41.0 | 4.48e-01 | 100.0% | 78.3% |
| 4507405 | 375.1.1.128 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_SprT | 0.65 | 38.0 | 4.60e-01 | 91.9% | 95.6% |
| 5052150 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.63 | 43.0 | 4.81e-01 | 79.7% | 96.4% |
| 5065792 | 301.1.1.2 ↗ | a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 | 0.62 | 50.0 | 3.90e-01 | 86.5% | 54.8% |
| 4928795 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.61 | 37.0 | 4.38e-01 | 77.0% | 100.0% |
| 5027350 | 301.1.1.2 ↗ | a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 | 0.61 | 48.0 | 3.94e-01 | 86.5% | 62.3% |
| 4147528 | 4.1.1.307 ↗ | beta barrels › SH3 › SH3 › SH3 › PF26132 | 0.59 | 43.0 | 4.42e-01 | 78.4% | 100.0% |
| 3187671 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.59 | 42.0 | 4.61e-01 | 82.4% | 95.0% |
| 136413 | 375.1.1.2 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rubredoxin | 0.58 | 44.0 | 4.76e-01 | 79.7% | 98.3% |
| 4130667 | 302.1.1.1 ↗ | a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C | 0.58 | 43.0 | 3.88e-01 | 82.4% | 55.5% |
| 4990489 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.57 | 37.0 | 4.29e-01 | 78.4% | 100.0% |
| 3725441 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.57 | 42.0 | 4.58e-01 | 78.4% | 100.0% |
| 3722497 | 1.1.2.22 ↗ | beta barrels › cradle loop barrel › RIFT-related › double psi › IML1_N_fung | 0.57 | 43.0 | 4.08e-01 | 97.3% | 67.8% |
| 3404684 | 10.12.1.84 ↗ | beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom | 0.57 | 47.0 | 3.40e-01 | 91.9% | 67.6% |
| 5002952 | 304.4.1.82 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF3303 | 0.57 | 41.0 | 3.86e-01 | 77.0% | 84.4% |
| 3590261 | 822.3.1.1 ↗ | a+b two layers › GYF/BRK domain-like › conserved domain protein SP_1775 › conserved domain protein SP_1775 › DUF4649 | 0.56 | 36.0 | 3.80e-01 | 81.1% | 72.1% |
| 5047668 | 2003.1.5.0 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases | 0.56 | 44.0 | 3.10e-01 | 86.5% | 60.2% |
| 4448678 | 4.1.1.307 ↗ | beta barrels › SH3 › SH3 › SH3 › PF26132 | 0.56 | 44.0 | 4.40e-01 | 86.5% | 100.0% |
| 3406258 | 221.1.1.76 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 | 0.55 | 39.0 | 3.68e-01 | 74.3% | 75.6% |
| 3849943 | 221.1.1.76 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 | 0.55 | 38.0 | 3.14e-01 | 74.3% | 46.9% |
| 3705532 | 302.1.1.1 ↗ | a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C | 0.54 | 40.0 | 3.43e-01 | 82.4% | 53.8% |
| 3604145 | 4.1.1.0 ↗ | beta barrels › SH3 › SH3 › SH3 | 0.53 | 40.0 | 4.34e-01 | 100.0% | 98.3% |
| 3586126 | 221.1.1.76 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 | 0.53 | 37.0 | 3.21e-01 | 74.3% | 55.2% |
| 4229021 | 11.1.1.55 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Mo-co_dimer | 0.53 | 39.0 | 2.91e-01 | 78.4% | 43.2% |
| 4961328 | 206.1.1.267 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › IucA_IucC | 0.53 | 45.0 | 2.87e-01 | 100.0% | 43.2% |
| 4566976 | 375.14.2.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS2) | 0.53 | 29.0 | 3.69e-01 | 86.5% | 100.0% |
| 3597792 | 221.7.1.0 ↗ | a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 | 0.51 | 38.0 | 3.41e-01 | 81.1% | 59.1% |
| 4096418 | 206.1.1.16 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › IucA_IucC,FhuF | 0.51 | 43.0 | 2.77e-01 | 100.0% | 43.7% |
| 4567075 | 10.12.1.84 ↗ | beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom | 0.51 | 43.0 | 2.91e-01 | 95.9% | 47.7% |
| 3258706 | 812.1.1.0 ↗ | a+b duplicates or obligate multimers › MinE-like › Cell division protein MinE topological specificity domain › Cell division protein MinE topological specificity domain | 0.50 | 38.0 | 3.21e-01 | 83.8% | 54.1% |
| 3175359 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 39.0 | 3.23e-01 | 86.5% | 57.9% |
D2
medium
residues 212-265
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4g80T00 | 1.20.120.350 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C | 0.61 | 43.0 | 3.20e-01 | 74.1% | 84.2% |