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KU963248.1__AMS02728.1__SEA_YVONNETASTIC_184__00179

Bact-Vir

KU963248.1__AMS02728.1__SEA_YVONNETASTIC_184__00179

Identity

Accession:
KU963248 ↗
Kingdom:
phage

Quality

75.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Yvonnevirus› Gordonia_phage_Yvonnetastic

TaxID: 1821566

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-54
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d33A00 2.60.40.3080 Mainly Beta › Sandwich › Immunoglobulin-like › 0.78 61.0 5.04e-01 100.0% 47.9%
3ue3A02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.76 58.0 4.18e-01 82.7% 78.9%
4kgmA00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.74 64.0 4.18e-01 100.0% 47.8%
4ftxB01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.70 52.0 3.96e-01 86.5% 33.6%
2bmxB01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.68 47.0 3.33e-01 80.8% 22.7%
5x6vF00 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.67 48.0 3.72e-01 78.8% 33.9%
1yprA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.67 48.0 3.66e-01 84.6% 32.0%
5ck3C00 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.67 50.0 4.04e-01 82.7% 77.1%
1nrjA00 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.67 50.0 3.69e-01 84.6% 31.3%
3r7wB02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.66 49.0 3.85e-01 82.7% 36.4%
3r7wC02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.66 46.0 3.70e-01 82.7% 36.4%
1yk9A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.65 55.0 3.88e-01 100.0% 65.2%
2oo3A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.65 54.0 3.53e-01 100.0% 20.6%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.65 50.0 3.83e-01 98.1% 34.1%
1bu6O01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 53.0 3.48e-01 100.0% 64.5%
1ifqB00 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.64 50.0 3.79e-01 86.5% 79.7%
5x6vG00 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.64 46.0 3.50e-01 78.8% 31.1%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.64 54.0 4.77e-01 100.0% 68.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 52.0 4.46e-01 100.0% 55.4%
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.63 45.0 4.19e-01 100.0% 58.3%
4gn2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.63 45.0 2.95e-01 76.9% 99.2%
3eqvA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.63 47.0 3.63e-01 86.5% 41.4%
6x4tA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 53.0 4.18e-01 100.0% 59.1%
3klqA01 2.60.40.3050 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 54.0 4.16e-01 100.0% 45.4%
3ll3B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 49.0 3.35e-01 100.0% 27.8%
4jysB00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.61 50.0 4.09e-01 100.0% 67.5%
3h76A01 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.61 48.0 3.41e-01 90.4% 40.2%
3zwbA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.61 48.0 3.10e-01 90.4% 42.3%
3cjmA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.61 45.0 2.98e-01 82.7% 89.4%
3id6A01 3.30.420.220 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.61 50.0 4.11e-01 98.1% 86.8%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.61 50.0 4.24e-01 100.0% 54.3%
3gqqA00 2.70.50.40 Mainly Beta › Distorted Sandwich › Coagulation Factor XIII; Chain A, domain 1 › GMP phosphodiesterase, delta subunit 0.60 49.0 3.46e-01 100.0% 28.1%
1nj4A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.60 46.0 3.07e-01 88.5% 42.8%
2qlcA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.60 48.0 3.83e-01 100.0% 40.5%
2gnxA02 3.30.450.240 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.60 41.0 3.37e-01 82.7% 35.8%
3h7lA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 4.29e-01 100.0% 57.0%
3k59A07 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.59 42.0 3.21e-01 78.8% 88.0%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.57 49.0 4.26e-01 100.0% 88.1%
4dipH00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.57 47.0 3.78e-01 100.0% 68.9%
2oi2A01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.57 46.0 3.52e-01 98.1% 86.8%
3fedA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.57 49.0 3.29e-01 100.0% 97.7%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 46.0 3.98e-01 100.0% 68.0%
2daxA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.57 42.0 3.18e-01 82.7% 34.0%
3onhA01 3.10.290.20 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 0.56 43.0 3.39e-01 100.0% 39.6%
5eo9A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 49.0 3.89e-01 100.0% 55.1%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 40.0 3.09e-01 84.6% 73.6%
1yi9A02 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.53 40.0 3.12e-01 100.0% 33.6%
3isyA00 2.60.40.2360 Mainly Beta › Sandwich › Immunoglobulin-like › Intracellular proteinase inhibitor BsuPI 0.52 43.0 3.48e-01 100.0% 85.5%
3rosA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.52 40.0 2.67e-01 92.3% 59.0%
4i3vA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.51 45.0 2.87e-01 100.0% 28.3%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3184485 76.1.1.0 ↗ beta duplicates or obligate multimers › beta-Prism I › beta-Prism I › beta-Prism I 0.78 64.0 5.06e-01 100.0% 44.4%
3839866 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.75 63.0 5.31e-01 96.2% 98.9%
3709246 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.75 53.0 5.00e-01 100.0% 61.5%
3923859 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.74 62.0 4.97e-01 100.0% 48.0%
4928070 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.74 58.0 4.65e-01 100.0% 43.3%
4929090 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.74 57.0 4.25e-01 100.0% 33.3%
5050910 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.73 52.0 4.06e-01 78.8% 34.8%
3975813 223.3.1.2 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Peptidase_S11 0.72 50.0 3.53e-01 75.0% 76.5%
5001318 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.71 49.0 3.89e-01 78.8% 34.5%
5053097 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.70 59.0 4.97e-01 100.0% 92.6%
3909337 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.70 61.0 4.68e-01 100.0% 53.3%
5077363 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.68 49.0 3.76e-01 78.8% 78.5%
3270265 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.68 49.0 3.71e-01 82.7% 30.4%
5079770 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.68 48.0 3.77e-01 82.7% 33.3%
4438218 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.68 57.0 4.58e-01 100.0% 89.1%
4358998 223.3.1.2 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Peptidase_S11 0.68 47.0 3.48e-01 73.1% 91.1%
4998154 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.67 47.0 3.57e-01 78.8% 29.6%
3889864 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 46.0 4.60e-01 100.0% 70.9%
4420915 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 0.66 56.0 4.37e-01 100.0% 48.3%
3739712 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.66 46.0 3.56e-01 80.8% 30.8%
4558763 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.66 51.0 3.90e-01 88.5% 77.8%
4333681 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 0.66 54.0 4.30e-01 100.0% 48.3%
3404192 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.65 57.0 4.19e-01 100.0% 60.0%
3168516 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.65 49.0 3.59e-01 82.7% 28.7%
4946800 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.65 48.0 3.51e-01 82.7% 38.7%
4624615 303.1.1.1 ↗ a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.65 53.0 3.96e-01 100.0% 36.1%
3258907 223.2.1.1 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Profilin 0.64 46.0 3.56e-01 86.5% 31.5%
4020851 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 47.0 3.61e-01 84.6% 32.3%
3256878 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 47.0 3.54e-01 82.7% 29.7%
4018561 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.64 47.0 3.53e-01 82.7% 29.7%
3722450 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.64 46.0 3.43e-01 78.8% 29.0%
3497127 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 45.0 3.34e-01 82.7% 27.6%
4290748 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.63 46.0 3.15e-01 78.8% 22.5%
3472406 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.63 55.0 3.43e-01 100.0% 17.7%
3400015 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.63 44.0 3.42e-01 78.8% 30.8%
5034209 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 50.0 4.79e-01 100.0% 78.3%
4977897 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.63 47.0 3.60e-01 84.6% 79.3%
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 0.62 53.0 3.84e-01 100.0% 74.8%
5073557 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 46.0 3.48e-01 84.6% 75.7%
3313678 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 45.0 3.43e-01 84.6% 30.7%
3177841 221.1.1.52 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Ubiquitin_2 0.61 47.0 4.01e-01 100.0% 50.0%
5071765 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 46.0 3.60e-01 84.6% 81.6%
3407363 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.61 45.0 3.36e-01 82.7% 29.7%
3974688 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.61 43.0 4.42e-01 76.9% 80.0%
3173109 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 42.0 3.31e-01 76.9% 31.2%
3645411 223.1.1.79 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_NLP 0.60 50.0 3.42e-01 100.0% 75.9%
4977323 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 42.0 3.21e-01 78.8% 31.2%
3220755 10.12.1.97 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › CNBH_CNNM2_C 0.59 46.0 3.28e-01 90.4% 54.4%
3996654 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 39.0 3.20e-01 75.0% 32.7%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.58 47.0 4.58e-01 100.0% 96.7%
3892842 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.58 46.0 4.47e-01 100.0% 86.2%
3312745 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 49.0 3.57e-01 100.0% 54.4%
3702049 2485.1.1.12 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › SCO1-SenC 0.57 46.0 3.35e-01 92.3% 36.7%
5049518 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 42.0 3.33e-01 86.5% 79.8%
4275468 223.1.1.95 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › NtrY_N 0.57 42.0 3.03e-01 84.6% 64.1%
4091593 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.57 49.0 3.66e-01 100.0% 96.4%
3598676 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 48.0 3.32e-01 100.0% 36.8%
3607227 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.55 44.0 4.49e-01 96.2% 96.0%
4029586 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.55 44.0 3.36e-01 100.0% 49.3%
5008605 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.55 39.0 2.89e-01 78.8% 25.5%
3794632 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.52 39.0 2.95e-01 78.8% 76.4%
3219557 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.52 44.0 4.26e-01 100.0% 86.7%
3255230 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.52 42.0 3.12e-01 100.0% 98.8%