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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00383

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00383

Identity

Kingdom:
phage

Quality

79.0 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 16-101
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5mmjo00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.88 63.0 6.74e-01 74.4% 85.3%
1fewA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 65.0 5.04e-01 86.0% 69.9%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.80 64.0 6.16e-01 84.9% 87.4%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 62.0 5.44e-01 82.6% 69.9%
2xqyA01 3.30.500.50 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.79 65.0 5.02e-01 87.2% 42.1%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 64.0 6.00e-01 89.5% 85.7%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.77 62.0 5.61e-01 89.5% 64.7%
2fupA00 1.20.58.300 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › FlgN-like 0.76 64.0 5.59e-01 90.7% 87.4%
2gomA00 1.10.10.1270 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Sbi, C3 binding domain IV 0.76 48.0 5.58e-01 87.2% 90.2%
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.76 64.0 5.30e-01 89.5% 55.9%
3kbtA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 59.0 4.04e-01 89.5% 25.0%
8carA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.75 62.0 3.99e-01 88.4% 22.6%
3rkgA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.74 64.0 5.09e-01 93.0% 69.5%
2dnxA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 60.0 5.27e-01 89.5% 77.7%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 58.0 5.36e-01 83.7% 90.7%
1a7eA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.73 58.0 5.16e-01 94.2% 61.0%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 59.0 5.08e-01 88.4% 71.3%
2nr4A02 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.73 48.0 5.65e-01 86.0% 100.0%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.72 53.0 5.61e-01 89.5% 87.0%
4ecgA00 1.20.1420.20 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › M75 peptidase, HXXE motif 0.72 63.0 4.11e-01 95.3% 63.9%
7fhyB01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.71 62.0 4.28e-01 96.5% 28.5%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 61.0 5.84e-01 93.0% 85.7%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.71 61.0 5.41e-01 100.0% 65.9%
2i0mA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.71 59.0 5.51e-01 90.7% 84.0%
2p61A00 1.20.120.490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hypothetical protein TM1646-like domain 0.71 58.0 5.16e-01 94.2% 64.0%
2i0mA02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.70 60.0 5.76e-01 95.3% 96.0%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.70 55.0 5.24e-01 86.0% 85.3%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 58.0 5.67e-01 89.5% 97.8%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.69 59.0 5.57e-01 93.0% 88.2%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.69 55.0 5.28e-01 93.0% 74.7%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.69 58.0 5.29e-01 94.2% 70.0%
2yv7A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.69 57.0 4.92e-01 91.9% 60.1%
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 57.0 5.38e-01 94.2% 90.6%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.68 57.0 5.27e-01 93.0% 72.2%
2i9cA01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.67 52.0 4.82e-01 83.7% 88.3%
2qupA00 1.20.120.490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hypothetical protein TM1646-like domain 0.67 58.0 5.12e-01 94.2% 65.5%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.66 51.0 4.75e-01 82.6% 89.0%
1q0gA00 1.20.120.400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nickel-containing superoxide dismutase 0.65 50.0 4.55e-01 82.6% 71.8%
1w53A00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.63 46.0 4.72e-01 79.1% 78.6%
6vudA01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.62 49.0 4.54e-01 86.0% 90.8%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.61 51.0 5.01e-01 93.0% 91.2%
6bl6B01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.61 45.0 3.05e-01 77.9% 80.7%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.60 46.0 4.33e-01 84.9% 77.3%
2d2sA01 1.20.58.1210 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, N-terminal helical domain 0.60 53.0 4.81e-01 97.7% 77.6%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 51.0 3.80e-01 94.2% 45.5%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.59 52.0 4.92e-01 100.0% 80.4%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.58 50.0 4.24e-01 100.0% 81.5%
3c18A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.55 44.0 4.00e-01 88.4% 74.6%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5027758 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.86 67.0 5.41e-01 88.4% 45.8%
150489 601.1.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › CHASE3 0.81 65.0 5.65e-01 86.0% 62.2%
3596858 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.80 68.0 4.70e-01 89.5% 32.3%
4524825 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.79 63.0 6.11e-01 86.0% 75.8%
3183030 101.1.2.519 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7791 0.79 67.0 4.98e-01 90.7% 40.0%
3920960 604.8.1.2 ↗ alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo › Mitofilin 0.78 66.0 5.66e-01 89.5% 77.7%
3612915 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.77 66.0 6.15e-01 90.7% 91.4%
5071225 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 57.0 5.16e-01 88.4% 58.3%
3992590 603.1.1.110 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF26585 0.77 64.0 6.06e-01 89.5% 91.0%
1713219 601.4.1.5 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › HBM 0.77 62.0 5.65e-01 88.4% 66.4%
4567957 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.76 64.0 5.72e-01 88.4% 80.0%
3389546 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.76 63.0 6.50e-01 93.0% 95.0%
4981185 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.76 63.0 4.94e-01 89.5% 96.0%
3668856 604.5.1.7 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ALMT 0.76 64.0 5.73e-01 89.5% 82.6%
3973500 601.1.2.144 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › HBM 0.76 62.0 5.62e-01 89.5% 66.1%
3432902 603.1.1.5 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin-6_N 0.75 66.0 5.91e-01 93.0% 92.2%
4995305 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.74 64.0 6.22e-01 93.0% 93.7%
4647884 601.2.1.7 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › HBM 0.74 62.0 5.29e-01 90.7% 57.0%
3488077 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.74 64.0 6.21e-01 93.0% 93.7%
5083305 601.33.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.73 61.0 5.06e-01 100.0% 52.4%
5071514 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.73 54.0 5.75e-01 87.2% 90.7%
3241687 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.73 58.0 5.31e-01 86.0% 80.0%
3973510 601.4.1.5 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › HBM 0.73 58.0 5.05e-01 88.4% 56.9%
3411108 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.72 65.0 5.49e-01 97.7% 61.5%
4001318 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 58.0 6.12e-01 86.0% 98.7%
4883406 622.4.1.1 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Blo-t-5 0.72 60.0 5.43e-01 90.7% 79.3%
4024396 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.72 63.0 5.32e-01 93.0% 79.3%
5052922 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.72 59.0 5.29e-01 89.5% 65.0%
3714029 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 61.0 4.70e-01 93.0% 47.4%
5079439 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.71 58.0 5.38e-01 98.8% 70.5%
3766400 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.71 63.0 5.74e-01 94.2% 93.6%
4134971 603.1.1.225 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › SNARE, PF26585 0.71 61.0 4.75e-01 95.3% 65.4%
3770 601.29.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › TM1646-like › TM1646-like › DUF327 0.71 58.0 5.18e-01 94.2% 64.6%
3307044 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 60.0 5.66e-01 94.2% 81.9%
5051279 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 58.0 4.96e-01 93.0% 90.9%
3388493 633.10.1.15 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like › Transmemb_17 0.70 62.0 5.30e-01 98.8% 63.1%
5074998 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.69 62.0 4.71e-01 98.8% 46.2%
1500831 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.69 61.0 5.77e-01 97.7% 93.1%
5049145 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 57.0 5.49e-01 93.0% 90.9%
3786136 603.1.1.3 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › V-SNARE 0.68 58.0 5.27e-01 94.2% 80.0%
3242888 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.68 55.0 4.81e-01 93.0% 57.8%
3473655 5001.1.1.3 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_2 0.67 58.0 3.78e-01 95.3% 48.8%
4955279 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.66 57.0 4.32e-01 94.2% 79.5%
3214883 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.66 60.0 4.85e-01 98.8% 61.9%
3621681 604.1.1.139 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF7799 0.66 55.0 5.38e-01 93.0% 93.7%
3924801 109.4.1.1643 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RSLD_CPSF6 0.66 49.0 4.77e-01 88.4% 72.6%
3430030 192.8.1.397 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF4220 0.66 57.0 4.68e-01 98.8% 52.7%
3309583 604.12.1.65 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT_ATG1 0.65 54.0 5.58e-01 93.0% 98.8%
3396848 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.65 58.0 5.12e-01 98.8% 72.6%
3271459 4323.1.1.1 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.64 47.0 3.89e-01 75.6% 65.3%
4961847 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.64 46.0 3.42e-01 74.4% 38.1%
3981322 7018.1.1.4 ↗ few secondary structure elements › gp76 helical domain › gp76 helical domain › gp76 helical domain › YbhQ 0.64 48.0 4.84e-01 80.2% 85.9%
4927816 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.62 53.0 4.06e-01 96.5% 79.0%
5083098 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.61 55.0 5.22e-01 100.0% 93.0%