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group_I_intron_GIY-YIG_endonuclease
Euk-VirPithovirus_sibericum
group_I_intron_GIY-YIG_endonuclease__YP_009001269__Pithovirus_sibericum__1450746
Identity
- Accession:
- YP_009001269 ↗
- Protein ID:
- group_I_intron_GIY-YIG_endonuclease
- Kingdom:
- euk
Quality
59.0
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Pimascovirales›
Pithoviridae›
Alphapithovirus›
Pithovirus_sibericum
TaxID: 1450746
Cluster
View cluster (2 members)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 3-103
Domain cluster:
rep: HQ317390.1__AFK66689.1__COPG_00093__00093__D5-82
CATH (45)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4dohE02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.72 | 40.0 | 3.97e-01 | 88.1% | 51.9% |
| 1y6kR02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.72 | 40.0 | 4.06e-01 | 88.1% | 53.4% |
| 1n26A02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.71 | 35.0 | 3.99e-01 | 80.2% | 61.5% |
| 1iarB02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.70 | 39.0 | 4.11e-01 | 88.1% | 59.8% |
| 2qsdA01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.68 | 39.0 | 4.62e-01 | 79.2% | 83.6% |
| 1blwA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.68 | 42.0 | 4.27e-01 | 93.1% | 61.8% |
| 6brbD00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.67 | 36.0 | 3.83e-01 | 82.2% | 58.6% |
| 2ekjA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.67 | 37.0 | 3.65e-01 | 84.2% | 50.5% |
| 4wtxA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.66 | 36.0 | 3.73e-01 | 82.2% | 54.6% |
| 3v6oA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.66 | 36.0 | 3.89e-01 | 86.1% | 60.9% |
| 4dohB02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.66 | 38.0 | 4.04e-01 | 89.1% | 64.8% |
| 4eq3A02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.65 | 44.0 | 4.34e-01 | 92.1% | 64.8% |
| 3lzqA00 | 2.60.40.2480 | Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type | 0.65 | 45.0 | 3.87e-01 | 87.1% | 45.2% |
| 3bpnC03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.65 | 42.0 | 4.24e-01 | 92.1% | 65.3% |
| 2h41A00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.64 | 36.0 | 3.72e-01 | 85.1% | 56.8% |
| 1cfbA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.62 | 36.0 | 3.61e-01 | 84.2% | 54.7% |
| 5dm6100 | 2.20.28.120 | Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › Ribosomal protein L33 | 0.62 | 32.0 | 4.08e-01 | 74.3% | 90.7% |
| 3r8qA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.62 | 34.0 | 3.62e-01 | 87.1% | 58.7% |
| 8afoA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.61 | 36.0 | 3.85e-01 | 92.1% | 65.9% |
| 5bncB01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.61 | 36.0 | 3.23e-01 | 81.2% | 39.6% |
| 1ci0B00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.59 | 40.0 | 3.20e-01 | 86.1% | 34.3% |
| 2i51B00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.59 | 40.0 | 3.21e-01 | 81.2% | 36.1% |
| 3kalB05 | 3.30.1490.50 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Glutathione synthase lid domain | 0.58 | 25.0 | 3.26e-01 | 74.3% | 67.8% |
| 1jx4A04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.58 | 37.0 | 3.75e-01 | 81.2% | 65.3% |
| 6julA02 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.57 | 36.0 | 3.72e-01 | 81.2% | 65.6% |
| 1flmA00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.57 | 37.0 | 3.50e-01 | 82.2% | 54.1% |
| 2i02A00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 36.0 | 3.27e-01 | 84.2% | 45.0% |
| 5escA00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 37.0 | 3.53e-01 | 87.1% | 56.3% |
| 8ct0B01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 42.0 | 3.61e-01 | 96.0% | 49.4% |
| 3mfiA04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.55 | 40.0 | 3.86e-01 | 86.1% | 65.5% |
| 1wv4B00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.55 | 38.0 | 3.35e-01 | 85.1% | 46.8% |
| 2htdB00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.55 | 36.0 | 3.41e-01 | 87.1% | 54.0% |
| 4u7cB04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.53 | 37.0 | 3.64e-01 | 87.1% | 66.1% |
| 6kjcA00 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.53 | 40.0 | 2.74e-01 | 81.2% | 76.0% |
| 5hdwA00 | 2.60.40.1470 | Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain | 0.53 | 34.0 | 3.19e-01 | 86.1% | 49.6% |
| 1rz1A00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.53 | 43.0 | 3.76e-01 | 87.1% | 90.1% |
| 7ylrA01 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.53 | 37.0 | 3.73e-01 | 81.2% | 71.4% |
| 4f07E00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.53 | 43.0 | 3.76e-01 | 87.1% | 90.6% |
| 4l82A00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.52 | 42.0 | 3.62e-01 | 87.1% | 90.4% |
| 2qckA01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 42.0 | 3.65e-01 | 87.1% | 92.1% |
| 3e4vA01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 40.0 | 3.40e-01 | 96.0% | 49.4% |
| 3bpkA01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 42.0 | 3.47e-01 | 88.1% | 92.2% |
| 1vl7A00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 35.0 | 3.28e-01 | 91.1% | 54.1% |
| 3ba3B00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 42.0 | 3.77e-01 | 90.1% | 72.7% |
| 1rfeA01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.51 | 40.0 | 3.62e-01 | 84.2% | 71.3% |
ECOD (46)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3870843 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.68 | 40.0 | 3.66e-01 | 92.1% | 44.6% |
| 3198986 | 72.1.1.0 ↗ | beta sandwiches › gamma-Crystallin-like › gamma-Crystallin-like › gamma-Crystallin-like | 0.68 | 39.0 | 3.86e-01 | 78.2% | 53.8% |
| 4983111 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.68 | 39.0 | 4.41e-01 | 85.1% | 76.0% |
| 3957374 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.67 | 40.0 | 4.64e-01 | 77.2% | 84.3% |
| 990538 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.66 | 38.0 | 4.05e-01 | 89.1% | 63.3% |
| 5068693 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.66 | 40.0 | 3.96e-01 | 85.1% | 57.1% |
| 3540762 | 11.1.1.129 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Interfer-bind | 0.66 | 38.0 | 3.67e-01 | 89.1% | 49.6% |
| 4075642 | 382.1.1.7 ↗ | few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Toxin_cobra-type | 0.64 | 31.0 | 3.80e-01 | 88.1% | 71.9% |
| 3620151 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.63 | 37.0 | 3.55e-01 | 82.2% | 49.6% |
| 3397499 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.61 | 45.0 | 4.16e-01 | 85.1% | 60.0% |
| 3267956 | 11.1.1.1311 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28708 | 0.61 | 37.0 | 3.49e-01 | 85.1% | 49.2% |
| 3957429 | 1.1.5.15 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red | 0.60 | 40.0 | 3.80e-01 | 82.2% | 57.1% |
| 3992265 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.60 | 36.0 | 4.09e-01 | 90.1% | 81.3% |
| 3925549 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.59 | 38.0 | 3.89e-01 | 88.1% | 66.0% |
| 4931996 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.58 | 37.0 | 3.39e-01 | 86.1% | 48.1% |
| 3262371 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.58 | 37.0 | 3.66e-01 | 88.1% | 60.0% |
| 2706608 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.57 | 37.0 | 3.49e-01 | 87.1% | 53.2% |
| 3259237 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.57 | 41.0 | 4.52e-01 | 85.1% | 96.2% |
| 3976579 | 11.1.1.227 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arylsulfotran_N | 0.57 | 32.0 | 3.25e-01 | 85.1% | 53.0% |
| 3641871 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.57 | 38.0 | 3.31e-01 | 85.1% | 43.1% |
| 4932075 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.56 | 37.0 | 3.42e-01 | 87.1% | 51.5% |
| 4233298 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.56 | 43.0 | 3.65e-01 | 96.0% | 48.8% |
| 3587296 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.56 | 46.0 | 4.27e-01 | 92.1% | 69.2% |
| 3276129 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.56 | 43.0 | 4.51e-01 | 81.2% | 98.9% |
| 3026889 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.56 | 42.0 | 3.52e-01 | 96.0% | 46.1% |
| 5036164 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.55 | 35.0 | 3.39e-01 | 87.1% | 54.8% |
| 4505054 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.55 | 43.0 | 3.64e-01 | 96.0% | 50.9% |
| 304148 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.55 | 36.0 | 3.41e-01 | 87.1% | 54.0% |
| 4452137 | 1.1.7.7 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 | 0.55 | 43.0 | 3.96e-01 | 85.1% | 68.1% |
| 4318524 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.55 | 41.0 | 3.55e-01 | 96.0% | 49.7% |
| 3604671 | 1.1.5.8 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx | 0.55 | 36.0 | 3.25e-01 | 85.1% | 48.2% |
| 3581307 | 382.1.1.0 ↗ | few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like | 0.55 | 32.0 | 3.74e-01 | 94.1% | 84.3% |
| 3387649 | 1.1.5.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel | 0.54 | 36.0 | 3.36e-01 | 85.1% | 51.1% |
| 5040595 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.54 | 41.0 | 3.61e-01 | 95.0% | 53.1% |
| 4512371 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.54 | 40.0 | 3.52e-01 | 95.0% | 51.2% |
| 3290160 | 4.1.1.323 ↗ | beta barrels › SH3 › SH3 › SH3 › WYL | 0.53 | 30.0 | 3.35e-01 | 81.2% | 70.0% |
| 4551218 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.53 | 43.0 | 3.63e-01 | 87.1% | 85.5% |
| 3839173 | 3019.1.1.0 ↗ | beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain | 0.52 | 45.0 | 3.51e-01 | 100.0% | 52.1% |
| 5024463 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.52 | 42.0 | 3.47e-01 | 87.1% | 85.4% |
| 5017812 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.52 | 41.0 | 3.39e-01 | 96.0% | 46.3% |
| 3744150 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.51 | 40.0 | 3.35e-01 | 95.0% | 46.7% |
| 4482805 | 1.1.5.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Flavin_Reduct | 0.51 | 41.0 | 3.36e-01 | 88.1% | 86.2% |
| 3718504 | 11.1.1.41 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C | 0.51 | 39.0 | 3.27e-01 | 81.2% | 85.7% |
| 5033505 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 35.0 | 3.41e-01 | 86.1% | 63.6% |
| 3280742 | 1.1.5.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel | 0.51 | 39.0 | 3.34e-01 | 83.2% | 62.4% |
| 3388466 | 11.1.1.41 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C | 0.51 | 38.0 | 3.34e-01 | 80.2% | 95.5% |
D2
high
residues 167-235