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SRR1747026_scaffold_22_prodigal-single.1__X__X__00070

Bact-Vir

SRR1747026_scaffold_22_prodigal-single.1__X__X__00070

Identity

Kingdom:
phage

Quality

65.5 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 medium residues 54-150_172-229_376-416
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19782.5 best DUF6267 59.6 5.10e-16 82.1% 43.6%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2hivA02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.58 49.0 4.85e-01 88.8% 88.3%
6rarI01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.58 48.0 4.83e-01 86.2% 91.8%
6imjA01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.56 46.0 4.78e-01 86.2% 90.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4943522 206.1.3.23 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RNA_ligase 0.62 50.0 4.80e-01 93.4% 75.0%
4995764 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.60 53.0 4.95e-01 91.8% 89.4%
193072 206.1.3.23 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RNA_ligase 0.58 51.0 4.84e-01 93.4% 86.8%
5077223 206.1.3.23 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RNA_ligase 0.57 53.0 4.20e-01 100.0% 64.9%
D2 medium residues 151-171_230-263_334-375
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 41.0 4.56e-01 78.4% 87.7%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.60 40.0 4.60e-01 73.2% 91.5%
2yf4F00 1.10.3420.10 Mainly Alpha › Orthogonal Bundle › putative ntp pyrophosphohydrolase like fold › putative ntp pyrophosphohydrolase like domain 0.58 41.0 3.62e-01 73.2% 96.5%
6gy8A01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.56 42.0 2.85e-01 78.4% 65.7%
6ldkA01 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.55 41.0 3.40e-01 78.4% 52.9%
2kg7B00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.53 39.0 3.95e-01 78.4% 87.6%
3qokA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.52 22.0 2.27e-01 94.8% 37.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3595149 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.73 42.0 5.31e-01 74.2% 93.3%
1821875 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.67 37.0 4.77e-01 73.2% 91.5%
5079107 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 37.0 3.42e-01 78.4% 81.5%
D3 medium residues 264-333
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dd9A03 1.20.50.20 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › DnaG, RNA polymerase domain, helical bundle 0.77 51.0 5.56e-01 85.7% 81.4%
2vtyA00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.73 54.0 4.26e-01 94.3% 38.2%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 49.0 4.23e-01 70.0% 50.0%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.72 49.0 3.91e-01 70.0% 39.3%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 46.0 4.61e-01 70.0% 69.9%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 53.0 5.63e-01 94.3% 95.2%
3eupB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.66 46.0 3.33e-01 72.9% 52.0%
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.65 41.0 4.89e-01 82.9% 97.7%
2py6A01 1.20.1270.160 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.65 40.0 3.96e-01 87.1% 58.9%
5u9nB00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.64 55.0 4.70e-01 100.0% 90.0%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.63 51.0 4.21e-01 92.9% 88.1%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.63 52.0 5.12e-01 98.6% 84.4%
3mvcB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.62 51.0 4.06e-01 94.3% 81.8%
2a0uB01 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 4.20e-01 100.0% 70.0%
2y8nA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.62 50.0 2.81e-01 88.6% 64.6%
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 47.0 4.55e-01 91.4% 72.2%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.61 50.0 4.10e-01 92.9% 59.0%
2hjmA01 1.20.120.460 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › protein pf1176 like 0.59 49.0 4.60e-01 92.9% 94.2%
6vxcA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.58 46.0 2.66e-01 90.0% 63.8%
2fzfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 50.0 3.97e-01 98.6% 87.3%
1u00A02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.58 40.0 3.65e-01 72.9% 58.3%
2w43A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 42.0 4.44e-01 90.0% 98.2%
1twcA01 4.10.860.120 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › RNA polymerase II, clamp domain 0.57 43.0 3.57e-01 82.9% 74.2%
7bi4A01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.57 37.0 2.81e-01 97.1% 25.3%
2hsbA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.56 45.0 3.76e-01 88.6% 75.4%
1rp3G02 1.20.140.160 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › PhyR, sigma-like (SL) domain 0.56 41.0 3.38e-01 81.4% 90.1%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.55 48.0 4.35e-01 98.6% 72.2%
7k3zG01 3.50.7.10 Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL 0.55 44.0 3.18e-01 90.0% 46.0%
5ymrC00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.55 43.0 2.49e-01 90.0% 63.7%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 46.0 3.88e-01 98.6% 83.1%
1wfdA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.54 45.0 4.12e-01 98.6% 71.0%
2pkeA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.51 44.0 4.28e-01 98.6% 94.9%
3gzkA02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 43.0 2.71e-01 100.0% 25.7%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.51 44.0 4.03e-01 95.7% 85.6%
3d0wA00 1.10.760.20 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Protein of unknown function DUF3243 0.50 44.0 4.12e-01 100.0% 80.2%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3576658 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.78 59.0 6.60e-01 90.0% 100.0%
3456467 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.71 61.0 5.77e-01 97.1% 85.9%
4990793 4144.1.1.0 ↗ alpha duplicates or obligate multimers › YejL-like › YejL-like › YejL-like 0.70 47.0 5.03e-01 84.3% 81.4%
5048590 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.69 47.0 4.02e-01 70.0% 49.1%
4956012 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.68 48.0 4.17e-01 74.3% 53.3%
4261003 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.67 42.0 5.01e-01 94.3% 97.8%
3592632 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.67 58.0 5.18e-01 92.9% 78.9%
3435543 192.15.1.77 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › OST3_OST6 0.67 51.0 4.34e-01 82.9% 89.6%
3396140 192.14.1.1 ↗ alpha bundles › Long alpha-hairpin › Siah interacting protein N terminal domain-like › Siah interacting protein N terminal domain-like › Siah-Interact_N 0.66 46.0 5.07e-01 97.1% 92.7%
3664301 5069.1.3.60 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › OST3_OST6 0.65 51.0 4.38e-01 85.7% 91.3%
3285603 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.65 55.0 3.79e-01 94.3% 74.6%
3792916 639.2.1.0 ↗ alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) 0.64 54.0 5.27e-01 91.4% 86.7%
4957532 3755.3.1.637 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF7121 0.64 47.0 3.82e-01 77.1% 58.5%
4446039 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.64 45.0 4.59e-01 95.7% 75.7%
3225080 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.63 57.0 4.64e-01 98.6% 94.4%
3385836 601.1.1.138 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › DUF4118 0.62 50.0 4.41e-01 98.6% 58.2%
5008666 192.6.1.12 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › PF27306 0.62 48.0 4.60e-01 100.0% 71.8%
3597965 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.62 45.0 3.18e-01 78.6% 29.8%
5009328 150.1.1.207 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF2175 0.62 47.0 4.11e-01 81.4% 81.9%
3473298 3277.2.1.1 ↗ alpha arrays › Thymine dioxygenase JBP1 DNA-binding domain-like › a C-terminal domain in chromodomain helicase DNA-binding protein 1 › a C-terminal domain in chromodomain helicase DNA-binding protein 1 › CHD1-like_C 0.60 50.0 4.25e-01 91.4% 62.6%
5034673 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.60 52.0 4.12e-01 98.6% 94.0%
3373860 109.4.1.1257 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2 0.60 48.0 3.31e-01 95.7% 24.8%
4023439 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.59 48.0 4.80e-01 98.6% 88.6%
3222259 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.59 49.0 3.12e-01 92.9% 94.1%
3306315 109.4.1.189 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 0.59 46.0 4.18e-01 85.7% 82.1%
5012651 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.57 46.0 4.37e-01 90.0% 84.7%
4618995 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.57 48.0 4.31e-01 94.3% 87.0%
5050430 109.32.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Alkylsulfatase SdsA1 linker domain › Alkylsulfatase SdsA1 linker domain › Alkyl_sulf_dimr 0.57 46.0 4.15e-01 94.3% 90.5%
4405472 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.56 42.0 3.59e-01 84.3% 98.4%
3613445 7563.1.1.2 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › Lysine_decarbox 0.56 48.0 3.23e-01 97.1% 31.9%
3938011 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.53 46.0 3.85e-01 98.6% 83.2%
4568335 3812.1.1.8 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › DUF5398 0.52 43.0 4.40e-01 97.1% 94.2%
3981456 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.50 42.0 2.47e-01 100.0% 33.1%
D4 medium residues 417-446_463-528
PDB
D5 medium residues 564-719
PDB
D6 medium residues 720-836
PDB
D7 medium residues 837-921
PDB