Back to structures

NC_060133.1__YP_010246209.1__L3Y21_gp096__00096

Bact-Vir

NC_060133.1__YP_010246209.1__L3Y21_gp096__00096

Identity

Accession:
NC_060133 ↗
Kingdom:
phage

Quality

92.0 mean pLDDT

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 174-237
PDB
CATH (59)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ne5B04 6.10.140.730 Special › Helix non-globular › Helix Hairpins › 0.86 63.0 6.97e-01 78.1% 96.1%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.78 57.0 4.94e-01 78.1% 54.6%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.76 57.0 5.55e-01 81.2% 76.4%
3bgeA01 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.76 55.0 4.84e-01 82.8% 52.1%
2qf9A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 49.0 3.69e-01 70.3% 85.9%
1iurA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.72 52.0 5.24e-01 76.6% 93.7%
3ztaA00 1.10.490.130 Mainly Alpha › Orthogonal Bundle › Globin-like › 0.72 63.0 4.97e-01 100.0% 73.4%
1mhyG02 1.20.1280.30 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 2 0.72 52.0 5.02e-01 78.1% 71.2%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.72 64.0 5.71e-01 100.0% 80.9%
1hu3A00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.71 60.0 4.23e-01 96.9% 38.7%
3e3vA03 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 0.70 53.0 5.61e-01 79.7% 92.9%
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.70 52.0 4.45e-01 78.1% 69.0%
4pxoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.70 59.0 4.69e-01 95.3% 73.3%
1q6aA00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.69 52.0 4.46e-01 82.8% 55.1%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.68 52.0 4.98e-01 82.8% 80.0%
7xcnM01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.68 57.0 5.43e-01 96.9% 98.7%
6t0bf00 1.25.40.40 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI 0.68 58.0 5.04e-01 98.4% 65.7%
3nkyA03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.68 55.0 5.29e-01 100.0% 79.5%
1v9mA01 1.10.132.50 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › ATP synthase (C/AC39) subunit, domain 3 0.67 48.0 4.00e-01 76.6% 72.2%
2ouwB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.67 59.0 4.65e-01 100.0% 57.4%
3ebbA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.67 57.0 3.81e-01 98.4% 25.0%
7wf8B01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.66 49.0 3.91e-01 89.1% 41.3%
5dikA00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.66 56.0 4.69e-01 98.4% 55.4%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.66 54.0 4.69e-01 95.3% 77.4%
3pasA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.65 50.0 3.53e-01 82.8% 54.2%
2lsgA00 1.20.58.1280 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DNA repair protein Rev1, C-terminal domain 0.64 53.0 4.77e-01 98.4% 81.4%
7y4rB01 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.64 56.0 4.82e-01 100.0% 75.5%
4g10A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 54.0 4.30e-01 96.9% 66.2%
2kc7A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.63 50.0 4.35e-01 87.5% 57.6%
1gg4A01 3.90.190.20 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Mur ligase, C-terminal domain 0.63 55.0 4.37e-01 100.0% 54.4%
2zopA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.63 47.0 3.99e-01 82.8% 71.4%
3nynA03 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.63 45.0 4.17e-01 76.6% 72.8%
4eadA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.61 53.0 4.53e-01 100.0% 97.2%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.61 47.0 3.90e-01 89.1% 54.8%
3k9iA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.61 50.0 4.37e-01 95.3% 59.2%
3d8lA00 1.10.8.940 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein, phage p2 ORF12 0.60 41.0 3.71e-01 71.9% 91.2%
7ocsB01 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 0.60 50.0 3.80e-01 100.0% 46.2%
4ga6A02 1.20.970.50 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › 0.60 51.0 3.94e-01 98.4% 65.1%
2acxA01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.60 46.0 3.20e-01 87.5% 25.9%
4agsA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 48.0 3.91e-01 95.3% 68.1%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.59 49.0 4.86e-01 96.9% 89.6%
4iluA02 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.58 47.0 4.16e-01 100.0% 69.4%
1x3kA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 47.0 3.82e-01 100.0% 55.1%
1zvwA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 48.0 4.77e-01 96.9% 97.0%
4gtnA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.57 49.0 4.69e-01 100.0% 85.1%
4dvgB00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.57 47.0 3.18e-01 100.0% 27.5%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.56 47.0 3.57e-01 100.0% 44.9%
1q2lA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.56 41.0 2.85e-01 79.7% 52.2%
4ga4A01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.56 46.0 4.58e-01 100.0% 100.0%
4f55A01 1.10.10.2520 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Cell wall hydrolase SleB, domain 1 0.56 47.0 4.39e-01 93.8% 86.3%
1w3bB00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 47.0 2.99e-01 98.4% 23.9%
1oyjB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 45.0 3.77e-01 100.0% 63.2%
3rv0C02 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.55 39.0 3.00e-01 73.4% 69.4%
2f9iD00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.55 48.0 3.25e-01 100.0% 34.9%
7xpcA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 47.0 3.01e-01 100.0% 58.5%
1x46A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 45.0 3.54e-01 100.0% 70.7%
4muoA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.52 44.0 4.30e-01 100.0% 93.1%
2c0kB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 41.0 3.37e-01 100.0% 57.0%
5c00D00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 41.0 2.98e-01 89.1% 82.7%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5039930 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.82 62.0 3.92e-01 79.7% 44.1%
3673343 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 0.78 53.0 4.51e-01 71.9% 46.7%
4034377 4982.1.1.2 alpha arrays › KaiA/RbsU domain-like › KaiA/RbsU domain › KaiA/RbsU domain › RsbU_N 0.76 59.0 5.23e-01 82.8% 68.9%
3283672 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.75 54.0 3.51e-01 76.6% 34.4%
4984330 3651.1.1.0 alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain 0.72 63.0 5.70e-01 100.0% 88.9%
3337098 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.72 62.0 5.53e-01 100.0% 94.7%
4452388 101.35.1.4 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.70 49.0 5.45e-01 73.4% 96.0%
3965020 102.1.2.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase 0.69 62.0 4.36e-01 100.0% 40.0%
5021492 608.1.1.1 alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.69 59.0 5.05e-01 98.4% 59.0%
3582570 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.69 57.0 3.71e-01 96.9% 20.7%
3717339 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 54.0 3.61e-01 87.5% 30.6%
3316034 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 59.0 4.00e-01 96.9% 27.1%
3236141 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.68 56.0 4.48e-01 95.3% 88.9%
3577067 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.68 57.0 4.55e-01 95.3% 90.8%
4946659 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.67 56.0 4.75e-01 95.3% 81.8%
3899614 109.4.1.2006 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT, PF29896 0.67 56.0 3.90e-01 100.0% 31.0%
5008560 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.66 56.0 4.85e-01 98.4% 74.3%
3399200 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.65 53.0 3.66e-01 90.6% 30.2%
3238600 633.2.1.0 alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.65 45.0 4.15e-01 73.4% 62.4%
165604 109.1.1.1 alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C 0.65 55.0 4.52e-01 96.9% 68.6%
5052083 601.28.1.0 alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.65 48.0 4.40e-01 79.7% 88.2%
3960348 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.62 53.0 5.05e-01 100.0% 82.7%
3834460 109.4.1.2069 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30216 0.62 52.0 3.70e-01 96.9% 47.6%
3226778 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.62 44.0 3.21e-01 78.1% 80.5%
4948367 4002.1.1.0 alpha bundles › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes 0.61 52.0 3.62e-01 96.9% 82.8%
3958866 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.61 43.0 3.33e-01 81.2% 32.7%
5051840 601.28.1.0 alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.59 42.0 3.91e-01 76.6% 85.9%
3913629 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.58 51.0 4.74e-01 100.0% 80.0%
5000247 184.1.1.0 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N 0.58 49.0 4.93e-01 96.9% 98.5%
3233722 631.1.1.1 alpha arrays › Glycolipid transfer protein, GLTP › Glycolipid transfer protein, GLTP › Glycolipid transfer protein, GLTP › GLTP 0.57 45.0 3.14e-01 87.5% 95.0%
3315665 109.4.1.1146 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_PUB 0.56 49.0 3.88e-01 100.0% 52.1%
4076215 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.55 46.0 4.49e-01 100.0% 95.7%
4050209 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.54 45.0 4.42e-01 98.4% 90.0%
4355361 184.1.1.1 alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.53 43.0 4.30e-01 100.0% 95.7%
5016617 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.53 44.0 3.01e-01 100.0% 59.6%
3577893 603.1.1.135 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › UNC80 0.52 42.0 3.49e-01 100.0% 73.6%
D2 medium residues 3-157
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09250.17 best Prim-Pol 124.3 8.90e-36 93.5% 99.4%