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SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00341

Bact-Vir

SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00341

Identity

Kingdom:
phage

Quality

96.7 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 4-71
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ufvA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.72 66.0 5.76e-01 100.0% 78.8%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.69 47.0 4.50e-01 100.0% 61.5%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.66 50.0 4.57e-01 100.0% 61.8%
3bgeA01 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.66 56.0 5.06e-01 97.1% 72.9%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.65 55.0 4.97e-01 97.1% 84.5%
7z7vE01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.65 44.0 4.65e-01 72.1% 88.3%
6fhpD00 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.64 47.0 4.94e-01 79.4% 93.5%
1t5jA00 1.10.4080.10 Mainly Alpha › Orthogonal Bundle › ADP-ribosylglycohydrolase fold › ADP-ribosylation/Crystallin J1 0.64 55.0 3.65e-01 100.0% 35.9%
1tqgA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.64 56.0 4.89e-01 100.0% 81.0%
3kd4A02 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.63 55.0 4.22e-01 98.5% 64.4%
7cjsB01 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.63 54.0 3.89e-01 100.0% 79.8%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.63 54.0 4.46e-01 100.0% 52.7%
3rnrB00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.63 55.0 3.93e-01 100.0% 86.3%
7ccmB01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.63 48.0 3.82e-01 83.8% 55.2%
1t5oA01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.62 54.0 4.32e-01 100.0% 49.6%
2ongA01 1.50.10.130 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Terpene synthase, N-terminal domain 0.62 44.0 3.15e-01 82.4% 25.0%
1o0sA02 1.20.1370.30 Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › 0.62 46.0 3.99e-01 80.9% 52.8%
3zssA02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.61 49.0 4.77e-01 91.2% 87.3%
1ibcB00 3.30.70.1470 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Caspase-like 0.61 49.0 4.56e-01 89.7% 69.3%
1lm3B00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.61 51.0 4.55e-01 100.0% 88.7%
1zu2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 46.0 3.64e-01 86.8% 69.6%
3s63A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.60 52.0 4.86e-01 100.0% 79.5%
7zm7601 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.60 44.0 3.37e-01 80.9% 40.1%
2rekA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 46.0 3.49e-01 86.8% 41.3%
3tviA01 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.59 50.0 3.42e-01 100.0% 38.9%
1bbhA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.58 51.0 4.19e-01 100.0% 79.4%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.58 44.0 3.91e-01 83.8% 64.1%
4gbjC02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.58 48.0 3.93e-01 95.6% 84.4%
2lqgA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.58 39.0 3.23e-01 72.1% 55.8%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.58 48.0 4.49e-01 100.0% 75.3%
3w2zA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.58 48.0 3.62e-01 95.6% 92.1%
1pbwB00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.58 49.0 3.62e-01 98.5% 87.7%
3rkoG00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 45.0 4.05e-01 88.2% 86.0%
3ci6B00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.57 49.0 3.71e-01 95.6% 92.7%
1mhyG02 1.20.1280.30 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 2 0.57 44.0 4.30e-01 82.4% 87.7%
2ibdA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 49.0 3.85e-01 97.1% 69.4%
5xdcB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.57 48.0 4.21e-01 100.0% 73.9%
4i43B02 3.30.43.40 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain 0.57 45.0 3.84e-01 88.2% 56.1%
1nklA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.56 47.0 4.53e-01 98.5% 84.6%
2i2oA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 41.0 2.95e-01 79.4% 51.2%
2ysrA00 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 0.55 46.0 4.03e-01 94.1% 86.7%
1mkiA02 1.10.1500.10 Mainly Alpha › Orthogonal Bundle › Probable Glutaminase Ybgj; Chain: A, domain 2 › 0.55 45.0 3.68e-01 94.1% 94.2%
1e3pA02 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.54 45.0 4.26e-01 97.1% 75.9%
2q24A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 45.0 3.41e-01 97.1% 50.3%
1txuA02 1.20.1050.80 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › VPS9 domain 0.53 44.0 3.47e-01 97.1% 62.5%
1urvA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 42.0 3.34e-01 91.2% 86.4%
3g0oA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.50 44.0 3.68e-01 100.0% 85.1%
5my3A00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.50 40.0 3.06e-01 98.5% 87.9%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4984499 1030.1.1.0 ↗ alpha duplicates or obligate multimers › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 0.75 67.0 5.45e-01 100.0% 58.4%
3925909 371.1.1.0 ↗ few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.70 60.0 5.29e-01 94.1% 68.0%
4144324 3811.1.1.1 ↗ alpha bundles › Decorin-binding protein A › Decorin-binding protein A › Decorin-binding protein A › Decorin_bind 0.70 61.0 4.62e-01 100.0% 47.1%
3646770 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.70 62.0 5.55e-01 100.0% 77.9%
4014369 528.1.1.0 ↗ alpha bundles › ADP-ribosylglycohydrolase › ADP-ribosylglycohydrolase › ADP-ribosylglycohydrolase 0.69 62.0 3.92e-01 100.0% 38.8%
4948638 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.69 59.0 5.56e-01 95.6% 89.3%
4970859 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.68 60.0 5.32e-01 100.0% 81.0%
3274085 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.68 56.0 5.60e-01 100.0% 88.6%
4981575 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.67 58.0 4.73e-01 100.0% 67.4%
3821233 138.1.1.2 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › Rep_fac_C 0.67 56.0 5.16e-01 94.1% 87.8%
4947323 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.66 58.0 5.08e-01 100.0% 77.1%
5074606 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.66 58.0 5.13e-01 100.0% 79.0%
4947816 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.66 57.0 5.09e-01 100.0% 81.0%
3285524 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.66 50.0 4.03e-01 82.4% 99.3%
3242500 601.3.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › PTPLA 0.65 58.0 4.11e-01 100.0% 43.8%
5049088 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.65 57.0 4.89e-01 100.0% 76.4%
5001952 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.64 53.0 3.94e-01 91.2% 95.4%
3959976 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.64 50.0 3.88e-01 85.3% 84.0%
3287061 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.64 52.0 4.36e-01 91.2% 83.3%
3229732 6171.1.1.0 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases 0.64 46.0 4.01e-01 75.0% 84.0%
5061366 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.64 52.0 4.26e-01 92.6% 82.3%
5074120 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.63 55.0 4.98e-01 100.0% 85.3%
4949161 3281.1.2.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit 8 (Nqo8)-related › NADHdh 0.63 50.0 3.47e-01 89.7% 54.0%
5082348 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.63 55.0 4.20e-01 95.6% 99.3%
3973017 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.62 52.0 4.28e-01 97.1% 83.0%
3615697 601.1.1.78 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Oscp1 0.62 50.0 3.85e-01 91.2% 91.5%
3930936 1137.2.1.1 ↗ a+b two layers › Tetrapyrrole methylase C-terminal domain-like › GckA/TtuD-like domain 2 › GckA/TtuD-like domain 2 › MOFRL 0.62 53.0 3.68e-01 98.5% 96.2%
3467351 109.4.1.1455 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27814 0.62 55.0 3.66e-01 98.5% 27.7%
4957898 191.1.1.63 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_N 0.61 45.0 3.24e-01 100.0% 26.5%
3412611 189.1.1.0 ↗ alpha bundles › GTPase activation domain, GAP › GTPase activation domain, GAP › GTPase activation domain, GAP 0.61 55.0 3.56e-01 98.5% 36.8%
4099504 604.17.1.0 ↗ alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.61 47.0 4.91e-01 82.4% 100.0%
3419853 192.29.1.19 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Cornichon 0.61 51.0 4.11e-01 97.1% 71.7%
3834638 3579.1.1.1 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › Oxidored_q3 0.61 44.0 3.21e-01 76.5% 33.2%
3978907 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.61 52.0 4.84e-01 100.0% 81.1%
5018323 223.1.1.26 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_3 0.60 48.0 3.66e-01 89.7% 94.7%
4568123 219.1.1.79 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core2 0.60 43.0 3.35e-01 80.9% 58.9%
4018207 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.57 49.0 3.76e-01 100.0% 65.5%
3390844 109.4.1.27 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › W2 0.56 49.0 3.76e-01 100.0% 58.2%
3289554 106.1.1.11 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N 0.55 43.0 3.71e-01 89.7% 92.5%
4074440 11.1.1.154 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GlgE_dom_N_S 0.55 48.0 3.54e-01 100.0% 60.0%
3269592 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.54 48.0 4.48e-01 100.0% 82.4%
5067071 604.17.1.0 ↗ alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.53 42.0 4.28e-01 85.3% 93.8%
4290988 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.53 44.0 3.34e-01 94.1% 92.9%
4997858 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.53 43.0 3.32e-01 94.1% 91.8%
4024128 603.1.1.185 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27014 0.52 40.0 3.01e-01 86.8% 51.8%
4989270 629.1.1.1 ↗ alpha bundles › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › Nitrate_red_del 0.51 43.0 3.15e-01 97.1% 87.6%
4846601 603.5.1.1 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like › FlgN 0.50 37.0 3.18e-01 82.4% 76.2%