Back to structures

LacPavin_0818_WC40_scaffold_30711_prodigal-single.1__X__X__00422

Bact-Vir

LacPavin_0818_WC40_scaffold_30711_prodigal-single.1__X__X__00422

Identity

Kingdom:
phage

Quality

76.0 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 20-75
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.86 66.0 5.31e-01 82.1% 50.5%
1yqgA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.85 66.0 5.13e-01 82.1% 46.0%
4cxfA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.85 75.0 6.31e-01 94.6% 60.9%
1ss3A00 1.10.287.720 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Pollen allergen ole e 6 0.83 54.0 5.74e-01 73.2% 76.0%
4h8aB01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.82 57.0 5.61e-01 73.2% 68.3%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.81 58.0 5.32e-01 78.6% 59.2%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.81 58.0 5.29e-01 75.0% 59.7%
1jxhA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.80 62.0 3.99e-01 100.0% 19.0%
2hroA02 1.10.274.10 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › PtsI, HPr-binding domain 0.79 56.0 4.17e-01 73.2% 32.8%
2ahrA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.79 59.0 4.81e-01 82.1% 49.1%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.78 58.0 6.36e-01 98.2% 100.0%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.78 60.0 4.49e-01 82.1% 52.3%
3vayA02 1.20.120.1600 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.77 61.0 5.17e-01 83.9% 96.6%
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 0.77 65.0 5.43e-01 94.6% 55.3%
2h09A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.76 51.0 5.16e-01 80.4% 69.6%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.75 54.0 5.78e-01 80.4% 93.5%
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.75 61.0 4.38e-01 91.1% 38.7%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.74 64.0 4.03e-01 100.0% 19.6%
4s1hA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.73 65.0 4.01e-01 100.0% 18.8%
2h9dD00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.73 59.0 4.90e-01 96.4% 51.0%
6m36O01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.73 56.0 4.75e-01 85.7% 90.6%
3g2bA00 1.10.10.1150 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD) 0.72 48.0 4.14e-01 73.2% 43.3%
3looB01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.72 53.0 3.39e-01 100.0% 16.2%
3pqaB01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.71 61.0 3.86e-01 94.6% 37.5%
2irmA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.71 61.0 3.73e-01 100.0% 15.9%
2i5uA00 1.10.10.630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DnaD domain-like 0.68 56.0 5.03e-01 100.0% 66.2%
5zzjA02 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.67 58.0 3.63e-01 96.4% 69.4%
4yzgA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.64 53.0 3.42e-01 98.2% 19.7%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.63 50.0 3.89e-01 85.7% 58.5%
8h6qD01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.63 52.0 3.24e-01 98.2% 16.6%
1vibA00 1.10.287.120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Neurotoxin B-IV-like 0.62 50.0 5.09e-01 92.9% 90.9%
2q0yA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 45.0 3.51e-01 85.7% 33.3%
3c3dA02 1.10.8.240 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › CofD-like domain 0.58 46.0 3.98e-01 85.7% 77.3%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.57 45.0 4.29e-01 85.7% 100.0%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.56 41.0 3.76e-01 92.9% 59.0%
2yi9A05 1.20.1270.270 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › VP1, C-terminal extension domain 0.56 39.0 3.65e-01 100.0% 57.1%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.56 45.0 4.38e-01 89.3% 96.8%
3fdjA01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.55 43.0 3.51e-01 85.7% 90.8%
2p4vA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.55 44.0 3.99e-01 87.5% 82.9%
2ds2D01 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.54 39.0 3.93e-01 82.1% 80.7%
1v9mA02 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.54 41.0 3.51e-01 87.5% 96.0%
2wmmA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.53 40.0 4.30e-01 85.7% 93.9%
6ygiB01 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.53 45.0 3.36e-01 96.4% 65.8%
2m6bA00 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.52 42.0 3.14e-01 91.1% 34.0%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 39.0 3.73e-01 85.7% 100.0%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 40.0 3.71e-01 87.5% 67.6%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.51 41.0 3.97e-01 89.3% 82.8%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4162124 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.88 67.0 5.62e-01 80.4% 50.0%
3284058 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.85 71.0 6.05e-01 100.0% 58.8%
3174240 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.85 65.0 5.21e-01 82.1% 49.5%
1208317 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.84 74.0 5.75e-01 94.6% 47.8%
4623581 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.83 73.0 5.82e-01 94.6% 50.5%
3286823 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.82 64.0 4.95e-01 83.9% 44.2%
4136948 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.82 64.0 5.12e-01 83.9% 51.4%
4990523 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.82 63.0 5.20e-01 82.1% 51.6%
3966878 3721.1.1.1 alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › VIT1 0.81 57.0 5.25e-01 75.0% 58.6%
2389466 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.81 70.0 6.06e-01 94.6% 62.4%
4426296 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.81 71.0 5.64e-01 94.6% 50.5%
4972595 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.81 61.0 4.88e-01 87.5% 42.9%
3344802 6158.1.1.0 alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.80 68.0 6.45e-01 91.1% 80.0%
3328316 3721.1.1.1 alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › VIT1 0.80 56.0 5.19e-01 75.0% 58.6%
4234269 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.80 66.0 5.87e-01 100.0% 63.7%
4498700 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.80 69.0 5.62e-01 94.6% 53.0%
1247957 191.1.1.18 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_14 0.80 70.0 5.41e-01 94.6% 60.5%
3881712 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.80 66.0 4.86e-01 89.3% 40.7%
3188842 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.79 66.0 4.96e-01 89.3% 44.0%
5032477 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.78 65.0 5.16e-01 91.1% 50.0%
4210413 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.77 65.0 5.27e-01 91.1% 55.0%
3255785 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.77 65.0 5.10e-01 91.1% 50.0%
3685821 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.77 64.0 4.99e-01 91.1% 50.4%
4635506 230.3.1.1 a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.76 63.0 4.66e-01 98.2% 36.4%
4948274 164.1.1.1 alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.76 59.0 5.42e-01 85.7% 76.0%
3588797 4084.1.1.0 alpha bundles › ChaB-like › ChaB-like › ChaB-like 0.76 53.0 5.13e-01 78.6% 64.6%
4988048 3788.1.1.0 alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.75 55.0 5.39e-01 78.6% 75.0%
3483536 5059.1.1.0 alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter 0.74 59.0 4.61e-01 87.5% 45.8%
3587414 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.74 61.0 4.94e-01 91.1% 52.4%
3909952 129.1.1.0 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.74 66.0 4.10e-01 100.0% 31.1%
5075474 164.1.1.1 alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.74 58.0 5.21e-01 87.5% 71.2%
3810044 198.1.1.2 alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.70 54.0 5.02e-01 87.5% 73.3%
5060609 632.8.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.70 55.0 5.06e-01 92.9% 66.7%
3474051 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.69 53.0 4.96e-01 87.5% 68.9%
3256442 3721.1.1.1 alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › VIT1 0.69 55.0 4.97e-01 85.7% 77.3%
3473554 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.68 53.0 4.84e-01 89.3% 67.5%
3114 4230.1.1.3 alpha arrays › DnaD domain › DnaD domain › DnaD domain › DnaB_2 0.68 56.0 5.10e-01 100.0% 68.9%
3570117 375.6.1.2 few secondary structure elements › Rubredoxin-like › FlhC-like › FlhC-like › PF31275 0.64 52.0 5.09e-01 89.3% 93.3%
164592 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.62 45.0 3.41e-01 85.7% 30.1%
4991198 2.1.1.359 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HupF_HypC 0.61 47.0 3.91e-01 91.1% 80.9%
4987541 611.8.1.0 alpha bundles › N-cbl like › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 0.61 52.0 4.25e-01 98.2% 65.5%