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LacPavin_0818_WC40_scaffold_120392_prodigal-single.1__X__X__00111

Bact-Vir

LacPavin_0818_WC40_scaffold_120392_prodigal-single.1__X__X__00111

Identity

Kingdom:
phage

Quality

39.7 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 85-177
PDB
D2 medium residues 249-318
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1or7B01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.64 50.0 4.67e-01 88.6% 73.4%
1j78A05 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.64 48.0 5.10e-01 78.6% 100.0%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 52.0 4.89e-01 100.0% 95.5%
2ffjA01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.60 43.0 4.62e-01 80.0% 96.4%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.60 46.0 3.76e-01 82.9% 92.5%
5oklA01 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.60 45.0 4.03e-01 81.4% 76.2%
7pjdC01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.58 42.0 3.26e-01 78.6% 51.2%
4fd4A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 42.0 3.14e-01 84.3% 94.3%
3r31A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.56 44.0 3.04e-01 85.7% 70.8%
1htjF00 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.56 41.0 3.08e-01 78.6% 68.1%
6lcuA02 1.10.10.470 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Maltooligosyl trehalose synthase; domain 4 0.56 44.0 3.84e-01 84.3% 82.9%
1l5aA03 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.56 46.0 3.37e-01 92.9% 88.6%
1egdA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.56 40.0 3.22e-01 77.1% 66.0%
7w5lA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.55 42.0 2.88e-01 82.9% 64.2%
3broD00 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 38.0 3.08e-01 94.3% 38.1%
7wboA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 40.0 3.10e-01 81.4% 51.7%
4hzuS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.53 43.0 3.31e-01 90.0% 69.5%
1ez0B01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.53 40.0 2.65e-01 82.9% 62.8%
3cl3A01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.52 37.0 3.59e-01 78.6% 73.8%
2of7A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 46.0 3.69e-01 100.0% 95.7%
3ezuA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 38.0 2.85e-01 78.6% 78.0%
2janA02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.51 39.0 3.60e-01 98.6% 62.4%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None 0.61 42.0 2.96e-01 70.0% 51.4%
3470751 3755.3.1.297 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF9 0.58 46.0 3.54e-01 85.7% 90.0%
3605091 1189.1.1.1 alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › Trypan_glycop 0.55 40.0 2.54e-01 77.1% 90.7%
4934439 2004.1.1.198 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.55 46.0 2.88e-01 98.6% 62.9%
4586750 7524.1.1.1 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.55 43.0 3.09e-01 87.1% 71.2%
4956012 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.53 40.0 3.54e-01 81.4% 81.0%
1905928 7524.1.1.1 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.52 39.0 2.89e-01 85.7% 81.7%
1901952 7524.1.1.1 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.52 40.0 2.91e-01 85.7% 75.3%
3592316 7014.1.1.0 alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain 0.51 41.0 2.71e-01 91.4% 66.5%
1760269 3567.1.1.0 a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.51 36.0 3.10e-01 77.1% 83.6%
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 0.50 38.0 2.78e-01 82.9% 45.5%
D3 medium residues 319-379
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.80 69.0 6.28e-01 95.1% 72.8%
1eyvB00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.73 49.0 3.78e-01 77.0% 31.6%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.69 57.0 5.28e-01 93.4% 79.7%
2no4A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.68 52.0 4.91e-01 83.6% 74.7%
4i8oA03 1.10.8.1130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain 0.61 44.0 4.37e-01 80.3% 95.5%
1sg7A00 1.10.1740.70 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › ChaB 0.60 47.0 4.53e-01 91.8% 81.3%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.59 44.0 4.12e-01 98.4% 63.0%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.58 45.0 4.29e-01 90.2% 81.6%
4oa3A00 3.10.310.50 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.58 47.0 3.78e-01 100.0% 83.7%
1m5yA01 1.10.4030.10 Mainly Alpha › Orthogonal Bundle › Triger factor/SurA peptide-binding fold › Porin chaperone SurA, peptide-binding domain 0.57 41.0 3.27e-01 75.4% 80.6%
2yfkA02 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.51 37.0 2.69e-01 80.3% 83.7%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.51 42.0 3.93e-01 91.8% 89.5%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3824070 103.1.1.109 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF28551 0.66 56.0 5.56e-01 100.0% 92.3%
3876674 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.63 46.0 4.11e-01 78.7% 71.1%
3586132 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.60 43.0 3.82e-01 78.7% 57.9%
3917977 108.1.1.73 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.60 50.0 4.50e-01 98.4% 73.3%
3283536 3694.1.1.2 alpha bundles › Tail specific protease helical domain › Tail specific protease helical domain › Tail specific protease helical domain › Tricorn_C1 0.57 46.0 4.37e-01 95.1% 78.7%
5061328 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.56 50.0 4.82e-01 100.0% 98.6%
5043977 181.1.1.1 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 › SRP54_N 0.53 43.0 4.11e-01 100.0% 80.0%
5061334 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.52 47.0 4.28e-01 98.4% 83.7%
3944357 101.1.1.394 alpha arrays › HTH › HTH › Three-helical HTH › DUF4158 0.52 42.0 3.80e-01 90.2% 75.3%
3970705 632.15.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.52 46.0 4.21e-01 100.0% 96.2%
5058632 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.52 46.0 4.45e-01 100.0% 97.1%
5062669 632.23.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.52 45.0 4.29e-01 98.4% 97.3%
5061725 632.23.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.52 43.0 4.00e-01 95.1% 81.2%
5061756 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.51 46.0 4.11e-01 100.0% 81.2%
5049185 3883.1.1.1 alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.51 42.0 2.96e-01 98.4% 39.6%
5060848 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.50 41.0 4.17e-01 88.5% 100.0%
D4 medium residues 380-487
PDB
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2y1hB00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.60 40.0 2.94e-01 75.9% 27.5%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 40.0 3.30e-01 70.4% 62.6%
7w5lA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.58 51.0 3.94e-01 100.0% 72.0%
2or0B01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.58 41.0 3.99e-01 75.0% 82.3%
4jz6A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.57 51.0 3.91e-01 100.0% 75.1%
4x28C01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.57 41.0 3.98e-01 75.0% 89.9%
6l25A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.56 39.0 2.94e-01 76.9% 30.2%
2ff4A02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 39.0 3.32e-01 72.2% 73.6%
3gg7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.56 38.0 2.91e-01 75.0% 30.9%
5ekcF01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.56 49.0 3.67e-01 100.0% 64.2%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.55 35.0 3.99e-01 98.1% 86.1%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 38.0 3.46e-01 71.3% 71.7%
2awiA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.55 34.0 4.04e-01 93.5% 98.5%
1xwyA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.54 40.0 2.98e-01 76.9% 31.9%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 37.0 3.25e-01 71.3% 58.9%
5tpmB00 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.53 45.0 4.10e-01 100.0% 69.5%
2ef8A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.53 34.0 3.82e-01 90.7% 84.5%
3wurA00 1.20.1420.60 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › 0.52 36.0 3.19e-01 72.2% 59.9%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 36.0 3.77e-01 100.0% 79.8%
2pybA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 36.0 3.25e-01 71.3% 67.5%
6zhhA01 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.51 37.0 3.17e-01 76.9% 90.6%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4984052 2002.1.1.44 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.59 39.0 2.96e-01 76.9% 28.6%
3801455 193.1.1.0 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like 0.59 41.0 3.82e-01 72.2% 88.9%
3320244 53.1.1.4 beta duplicates or obligate multimers › Triple beta-spiral › Triple beta-spiral › Triple beta-spiral › XH 0.58 45.0 4.57e-01 100.0% 86.7%
3707113 109.6.1.1 alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF 0.57 41.0 3.08e-01 75.9% 81.7%
3959628 1075.1.2.0 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.56 40.0 3.53e-01 73.1% 97.5%
3273063 193.1.1.1 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › CH 0.56 40.0 3.79e-01 75.9% 83.0%
3229471 5001.1.1.106 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Str 0.56 41.0 2.99e-01 77.8% 79.1%
2879020 4033.1.1.0 alpha arrays › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like 0.55 40.0 4.04e-01 75.9% 94.3%
4586750 7524.1.1.1 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.54 48.0 3.79e-01 98.1% 80.8%
55837 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.53 37.0 3.23e-01 70.4% 58.5%
4198585 5059.1.1.2 alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Multi_Drug_Res 0.52 37.0 3.64e-01 84.3% 67.5%
3670373 5054.1.1.70 alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Yip1 0.51 43.0 4.31e-01 92.6% 91.8%
D5 medium residues 788-841_868-882
PDB
D6 medium residues 1151-1201_1667-1688_1700-1739
PDB
D7 medium residues 1796-1886_1934-1947
PDB