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group_I_intron_endonuclease
Euk-VirShrimp_hemocyte_iridescent_virus
group_I_intron_endonuclease__YP_010084782__Shrimp_hemocyte_iridescent_virus__2039780
Identity
- Accession:
- YP_010084782 ↗
- Protein ID:
- group_I_intron_endonuclease
- Kingdom:
- euk
Quality
72.9
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Pimascovirales›
Iridoviridae›
Decapodiridovirus›
Shrimp_hemocyte_iridescent_virus
TaxID: 2039780
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 13-97
Domain cluster:
rep: NC_031927.1__YP_009323018.1__BOW86_gp085__00085__D3-79
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01541.31 best | GIY-YIG | 29.6 | 9.50e-07 | 96.5% | 91.0% |
D2
high
residues 335-439
Domain cluster:
rep: BV_ODV-E26__YP_009666490__Lonomia_obliqua_multiple_nucleopolyhedrovirus__134394__D138-232
CATH (11)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2jrjA00 | 3.30.40.10 | Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) | 0.56 | 20.0 | 2.75e-01 | 82.9% | 57.7% |
| 3b73B00 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.54 | 35.0 | 3.72e-01 | 97.1% | 76.4% |
| 2e9xB01 | 3.40.5.50 | Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › | 0.53 | 29.0 | 3.51e-01 | 100.0% | 83.3% |
| 6oinA01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.53 | 29.0 | 3.48e-01 | 92.4% | 82.1% |
| 4gyiA01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.53 | 35.0 | 3.74e-01 | 96.2% | 77.4% |
| 1vs3A01 | 3.30.70.580 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, N-terminal subdomain | 0.53 | 39.0 | 3.92e-01 | 77.1% | 100.0% |
| 7vxrA01 | 3.40.800.10 | Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Ureohydrolase domain | 0.53 | 38.0 | 3.98e-01 | 82.9% | 82.7% |
| 2kdoA03 | 3.30.70.240 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.52 | 37.0 | 4.06e-01 | 80.0% | 97.5% |
| 2r4hC01 | 2.30.42.10 | Mainly Beta › Roll › Pdz3 Domain › PDZ domain | 0.52 | 31.0 | 3.40e-01 | 100.0% | 70.5% |
| 1t8rA01 | 3.30.1730.10 | Alpha Beta › 2-Layer Sandwich › amp nucleosidase, domain 1 › AMP nucleoside phosphorylase, N-terminal domain | 0.51 | 40.0 | 3.56e-01 | 83.8% | 68.9% |
| 2h5eA03 | 3.30.70.3280 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptide chain release factor 3, domain III | 0.51 | 45.0 | 4.20e-01 | 100.0% | 83.9% |
ECOD (16)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3946107 | 821.1.1.3 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › T5orf172 | 0.71 | 58.0 | 6.08e-01 | 100.0% | 97.9% |
| 4013514 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.63 | 39.0 | 3.97e-01 | 81.9% | 62.9% |
| 3285236 | 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 | 0.63 | 36.0 | 4.53e-01 | 95.2% | 100.0% |
| 4195119 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.58 | 44.0 | 3.39e-01 | 82.9% | 57.3% |
| 4309233 | 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 | 0.56 | 34.0 | 3.85e-01 | 98.1% | 84.0% |
| 4222499 | 101.19.1.0 ↗ | alpha arrays › HTH › C-terminal subdomain in oxygen-independent coproporphyrinogen III oxidase HemN › C-terminal subdomain in oxygen-independent coproporphyrinogen III oxidase HemN | 0.56 | 37.0 | 4.00e-01 | 97.1% | 80.0% |
| 4948782 | 101.1.2.136 ↗ | alpha arrays › HTH › HTH › winged helix domain › HTH_20 | 0.53 | 31.0 | 3.50e-01 | 90.5% | 78.7% |
| 3727693 | 5.1.5.62 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Beta-prop_LRRK2 | 0.53 | 38.0 | 2.61e-01 | 76.2% | 92.7% |
| 4961972 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.52 | 30.0 | 3.39e-01 | 93.3% | 73.8% |
| 3879122 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.52 | 39.0 | 3.67e-01 | 79.0% | 86.2% |
| 3891640 | 7.1.1.1 ↗ | beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ | 0.52 | 31.0 | 3.07e-01 | 100.0% | 53.9% |
| 4973418 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.52 | 34.0 | 3.92e-01 | 92.4% | 100.0% |
| 5010635 | 304.102.1.0 ↗ | a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase | 0.52 | 45.0 | 4.00e-01 | 100.0% | 98.1% |
| 5068452 | 101.1.2.30 ↗ | alpha arrays › HTH › HTH › winged helix domain › TrmB | 0.52 | 33.0 | 3.55e-01 | 97.1% | 77.6% |
| 3732370 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.51 | 30.0 | 3.73e-01 | 100.0% | 100.0% |
| 4992861 | 101.1.2.927 ↗ | alpha arrays › HTH › HTH › winged helix domain › DUF7347 | 0.51 | 30.0 | 3.15e-01 | 89.5% | 62.1% |
D3
medium
residues 126-249
Domain cluster:
rep: hypothetical_protein_KM509_gp097__YP_010084849__Shrimp_hemocyte_iridescent_virus__2039780__D36-143
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF10553.15 best | MSV199 | 25.4 | 2.10e-05 | 30.6% | 25.0% |
CATH (15)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2wteA02 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.66 | 27.0 | 3.55e-01 | 74.2% | 66.7% |
| 4dxwA02 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.59 | 44.0 | 4.64e-01 | 91.9% | 87.5% |
| 1r7jA00 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.58 | 39.0 | 4.56e-01 | 87.9% | 95.6% |
| 1v4aA03 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.57 | 39.0 | 3.68e-01 | 94.4% | 57.5% |
| 3fb2A01 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.56 | 35.0 | 3.72e-01 | 96.8% | 71.4% |
| 3lbxB01 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.55 | 38.0 | 4.03e-01 | 99.2% | 80.4% |
| 1fxkB00 | 1.10.287.370 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.55 | 40.0 | 4.25e-01 | 97.6% | 85.3% |
| 2k53A00 | 1.10.3910.10 | Mainly Alpha › Orthogonal Bundle › SP0561-like › SP0561-like | 0.55 | 27.0 | 3.44e-01 | 83.1% | 81.4% |
| 6vddA02 | 1.20.1060.10 | Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 | 0.54 | 41.0 | 4.23e-01 | 100.0% | 87.8% |
| 1s35A02 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.53 | 37.0 | 3.89e-01 | 100.0% | 80.0% |
| 2xfvA00 | 3.10.260.30 | Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › | 0.52 | 38.0 | 4.00e-01 | 75.0% | 89.8% |
| 1lnwF01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.52 | 41.0 | 4.18e-01 | 88.7% | 85.5% |
| 3mczA01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.51 | 26.0 | 3.17e-01 | 87.9% | 73.2% |
| 5y2vC01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.51 | 34.0 | 3.99e-01 | 73.4% | 100.0% |
| 2etdA00 | 1.20.1440.20 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › LemA-like domain | 0.51 | 44.0 | 4.25e-01 | 95.2% | 86.5% |
ECOD (10)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3916642 | 192.2.1.56 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › KIF9 | 0.64 | 41.0 | 3.89e-01 | 100.0% | 53.3% |
| 4968618 | 611.6.1.0 ↗ | alpha bundles › N-cbl like › PT26-6P helical domain › PT26-6P helical domain | 0.58 | 35.0 | 3.86e-01 | 99.2% | 75.5% |
| 3758972 | 604.1.1.1 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin | 0.57 | 39.0 | 4.14e-01 | 99.2% | 78.2% |
| 5071075 | 101.1.2.927 ↗ | alpha arrays › HTH › HTH › winged helix domain › DUF7347 | 0.56 | 38.0 | 4.46e-01 | 76.6% | 100.0% |
| 4038279 | 1037.1.1.1 ↗ | alpha bundles › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › Prolipoprotein diacylglyceryl transferase › LGT | 0.55 | 43.0 | 3.26e-01 | 82.3% | 62.4% |
| 3757568 | 604.1.1.1 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin | 0.54 | 38.0 | 4.08e-01 | 100.0% | 83.8% |
| 3229643 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.53 | 39.0 | 3.96e-01 | 98.4% | 78.3% |
| 4954786 | 605.1.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase | 0.53 | 35.0 | 4.06e-01 | 100.0% | 97.6% |
| 4224284 | 101.1.2.498 ↗ | alpha arrays › HTH › HTH › winged helix domain › PF25870 | 0.52 | 29.0 | 3.17e-01 | 79.0% | 65.0% |
| 3929429 | 5050.1.1.31 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › SLC52_ribofla_tr | 0.50 | 46.0 | 3.88e-01 | 100.0% | 98.0% |