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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00543
Bact-VirSR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00543
Identity
- Kingdom:
- phage
Quality
69.2
mean pLDDT
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 4-86
Domain cluster:
representative
CATH (39)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2dkmA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.70 | 47.0 | 4.42e-01 | 100.0% | 55.8% |
| 2qsdA01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.69 | 48.0 | 5.21e-01 | 100.0% | 91.0% |
| 2q7nA05 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.68 | 49.0 | 4.66e-01 | 100.0% | 64.3% |
| 4a18X01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.65 | 47.0 | 4.82e-01 | 77.1% | 78.5% |
| 1vwxS01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.65 | 46.0 | 4.93e-01 | 78.3% | 88.7% |
| 5kfzA04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.65 | 49.0 | 4.32e-01 | 80.7% | 56.1% |
| 1mvpA00 | 2.40.70.10 | Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases | 0.64 | 52.0 | 4.75e-01 | 100.0% | 66.1% |
| 2mfaA00 | 2.10.60.10 | Mainly Beta › Ribbon › CD59 › CD59 | 0.63 | 31.0 | 3.59e-01 | 74.7% | 64.9% |
| 4njcA00 | 3.10.20.730 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like | 0.62 | 39.0 | 4.40e-01 | 77.1% | 86.7% |
| 4hsaF02 | 2.60.40.2150 | Mainly Beta › Sandwich › Immunoglobulin-like › Interleukin-17 receptor A/B, fibronectin-III-like domain 2 | 0.61 | 49.0 | 4.57e-01 | 100.0% | 69.5% |
| 5c86A02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.59 | 46.0 | 4.33e-01 | 100.0% | 68.3% |
| 6x3aA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.59 | 46.0 | 4.35e-01 | 100.0% | 68.3% |
| 2mraA00 | 3.30.1710.10 | Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein | 0.59 | 51.0 | 4.66e-01 | 100.0% | 87.2% |
| 1x9tA02 | 3.90.1620.10 | Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 | 0.59 | 50.0 | 3.61e-01 | 100.0% | 67.1% |
| 1pfoA01 | 3.90.840.10 | Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain | 0.59 | 52.0 | 4.06e-01 | 100.0% | 52.5% |
| 1ksiA03 | 2.70.98.20 | Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain | 0.58 | 52.0 | 3.32e-01 | 100.0% | 83.4% |
| 3znuA00 | 3.30.70.1060 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel | 0.58 | 42.0 | 4.06e-01 | 77.1% | 91.5% |
| 5b71E00 | 2.60.40.1930 | Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain | 0.57 | 39.0 | 3.77e-01 | 100.0% | 62.4% |
| 3eipA00 | 3.10.50.20 | Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein | 0.56 | 40.0 | 4.05e-01 | 75.9% | 97.6% |
| 5jp0A03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 44.0 | 3.94e-01 | 100.0% | 58.9% |
| 2qlcA00 | 3.40.140.10 | Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 | 0.55 | 48.0 | 4.20e-01 | 97.6% | 77.0% |
| 5yotA03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 46.0 | 4.16e-01 | 100.0% | 66.7% |
| 5jtwA03 | 2.60.40.1940 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.55 | 47.0 | 4.18e-01 | 100.0% | 64.6% |
| 5tf0B03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 46.0 | 4.20e-01 | 100.0% | 70.3% |
| 4i3gA04 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 47.0 | 4.25e-01 | 100.0% | 70.2% |
| 6p3xB01 | 3.40.140.10 | Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 | 0.54 | 46.0 | 3.65e-01 | 95.2% | 67.8% |
| 4fcaA01 | 2.60.120.1250 | Mainly Beta › Sandwich › Jelly Rolls › Peptidase M60, enhancin-like domain 1 | 0.54 | 37.0 | 3.43e-01 | 100.0% | 54.1% |
| 2nmlA00 | 3.30.2260.10 | Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary | 0.54 | 48.0 | 4.52e-01 | 100.0% | 84.0% |
| 2wxfA02 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.54 | 48.0 | 4.30e-01 | 100.0% | 71.4% |
| 2bs2B01 | 3.10.20.30 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain | 0.54 | 47.0 | 4.41e-01 | 100.0% | 85.8% |
| 3bgaA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 43.0 | 3.91e-01 | 100.0% | 64.9% |
| 1hq6B00 | 3.50.20.10 | Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B | 0.54 | 45.0 | 3.41e-01 | 97.6% | 60.5% |
| 5i4dA02 | 2.40.50.110 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.53 | 26.0 | 2.71e-01 | 100.0% | 43.4% |
| 3up6A02 | 2.60.40.3380 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.53 | 46.0 | 3.79e-01 | 100.0% | 56.4% |
| 5z9sA03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 44.0 | 3.90e-01 | 100.0% | 64.2% |
| 7pjjA03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 43.0 | 3.82e-01 | 100.0% | 61.5% |
| 3f02B02 | 2.30.39.10 | Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 | 0.51 | 36.0 | 3.41e-01 | 74.7% | 94.0% |
| 6jhpA01 | 2.70.98.60 | Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › alpha-galactosidase from lactobacil brevis | 0.50 | 42.0 | 3.03e-01 | 100.0% | 84.2% |
| 1s3rA04 | 2.60.40.1430 | Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 | 0.50 | 40.0 | 3.72e-01 | 100.0% | 67.6% |
ECOD (43)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| None | — | 0.75 | 45.0 | 2.58e-01 | 100.0% | 6.9% | |
| 5013194 | 3115.4.1.0 ↗ | a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 | 0.74 | 48.0 | 5.67e-01 | 71.1% | 100.0% |
| 3586706 | 3792.1.1.2 ↗ | beta sandwiches › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › APC1_3rd | 0.73 | 45.0 | 4.38e-01 | 100.0% | 56.7% |
| 4942818 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.73 | 55.0 | 4.64e-01 | 92.8% | 47.9% |
| 5030993 | 3115.1.1.1 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A | 0.70 | 47.0 | 4.80e-01 | 75.9% | 72.5% |
| 2106284 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.69 | 49.0 | 5.39e-01 | 77.1% | 92.5% |
| 4084879 | 3115.1.1.1 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A | 0.66 | 47.0 | 4.68e-01 | 75.9% | 72.9% |
| 1442666 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.65 | 47.0 | 4.78e-01 | 77.1% | 76.5% |
| 1790231 | 244.1.1.4 ↗ | a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › DAO | 0.65 | 47.0 | 4.62e-01 | 75.9% | 94.4% |
| 3517068 | 3115.1.1.6 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 | 0.65 | 45.0 | 4.95e-01 | 75.9% | 92.3% |
| 3882782 | 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 | 0.65 | 48.0 | 4.22e-01 | 80.7% | 61.5% |
| 3593924 | 302.1.1.0 ↗ | a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain | 0.65 | 49.0 | 4.33e-01 | 80.7% | 55.8% |
| 3216289 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.64 | 46.0 | 4.41e-01 | 100.0% | 65.3% |
| 3229470 | 2003.1.3.1 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO | 0.64 | 47.0 | 3.14e-01 | 77.1% | 24.6% |
| 223776 | 3115.4.1.1 ↗ | a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 | 0.64 | 43.0 | 4.58e-01 | 77.1% | 80.3% |
| 3734418 | 4121.1.1.0 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like | 0.63 | 56.0 | 3.76e-01 | 100.0% | 49.4% |
| 4648475 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.63 | 43.0 | 4.83e-01 | 80.7% | 98.3% |
| 3 | 1.1.1.3 ↗ | beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP | 0.62 | 52.0 | 4.71e-01 | 100.0% | 67.0% |
| 3892842 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.61 | 43.0 | 4.67e-01 | 75.9% | 93.8% |
| 3987406 | 3115.6.1.1 ↗ | a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › RpoY | 0.61 | 44.0 | 4.55e-01 | 95.2% | 84.0% |
| 3208802 | 3435.1.1.3 ↗ | a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › CENP-L | 0.61 | 50.0 | 3.51e-01 | 90.4% | 39.0% |
| 4087729 | 221.1.1.97 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF508 | 0.60 | 52.0 | 4.98e-01 | 97.6% | 98.9% |
| 4237265 | 4.1.1.0 ↗ | beta barrels › SH3 › SH3 › SH3 | 0.59 | 47.0 | 4.33e-01 | 100.0% | 65.5% |
| 3282710 | 2492.1.1.35 ↗ | a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › DUF4192 | 0.59 | 50.0 | 4.10e-01 | 96.4% | 66.1% |
| 4867394 | 3820.1.1.1 ↗ | a+b complex topology › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › Cas9_PI | 0.58 | 41.0 | 3.86e-01 | 73.5% | 100.0% |
| 3333290 | 10.32.1.203 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin | 0.57 | 45.0 | 3.52e-01 | 85.5% | 76.1% |
| 1919639 | 245.1.1.0 ↗ | a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 | 0.57 | 38.0 | 3.73e-01 | 100.0% | 62.6% |
| 3982100 | 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 | 0.56 | 43.0 | 3.70e-01 | 88.0% | 60.7% |
| 3484366 | 284.1.2.1 ↗ | a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C | 0.55 | 44.0 | 4.15e-01 | 100.0% | 72.0% |
| 3251650 | 10.2.1.84 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Seipin | 0.55 | 44.0 | 3.64e-01 | 88.0% | 58.1% |
| 3824339 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.55 | 38.0 | 3.05e-01 | 74.7% | 37.0% |
| 3705745 | 221.13.1.0 ↗ | a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain | 0.55 | 49.0 | 4.21e-01 | 100.0% | 83.8% |
| 3919016 | 11.1.1.16 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Transglut_N | 0.54 | 47.0 | 3.99e-01 | 100.0% | 56.6% |
| 3256274 | 210.2.1.1 ↗ | a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C | 0.54 | 45.0 | 3.30e-01 | 100.0% | 65.1% |
| 4547058 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.54 | 48.0 | 3.67e-01 | 100.0% | 80.4% |
| 3417051 | 207.1.1.24 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_8 | 0.52 | 46.0 | 2.87e-01 | 100.0% | 21.4% |
| 3993633 | 2492.1.1.42 ↗ | a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB, MitMem_reg | 0.52 | 43.0 | 3.30e-01 | 97.6% | 47.0% |
| 3291916 | 2492.1.1.4 ↗ | a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like | 0.51 | 44.0 | 3.05e-01 | 100.0% | 26.7% |
| 5053865 | 821.1.1.0 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.51 | 44.0 | 4.32e-01 | 97.6% | 97.8% |
| 3990833 | 382.1.1.13 ↗ | few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Ly-6_related | 0.50 | 36.0 | 3.52e-01 | 77.1% | 83.2% |
| 4560677 | 206.1.3.19 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C | 0.50 | 41.0 | 3.00e-01 | 89.2% | 88.7% |
| 4155213 | 219.1.1.50 ↗ | a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH_1 | 0.50 | 44.0 | 2.79e-01 | 100.0% | 66.2% |
| 4014712 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 43.0 | 3.90e-01 | 100.0% | 83.3% |