Back to structures

LacPavin_0818_WC40_scaffold_86355_prodigal-single.1__X__X__00083

Bact-Vir

LacPavin_0818_WC40_scaffold_86355_prodigal-single.1__X__X__00083

Identity

Kingdom:
phage

Quality

81.0 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 6-55
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.91 62.0 4.65e-01 72.0% 31.9%
7yb9A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.84 62.0 3.95e-01 78.0% 23.4%
3l0iA01 1.20.120.1520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.84 74.0 4.98e-01 98.0% 30.7%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 57.0 6.07e-01 72.0% 83.7%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.83 65.0 4.78e-01 84.0% 52.9%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.81 55.0 5.73e-01 72.0% 93.5%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.80 54.0 5.02e-01 74.0% 56.2%
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.79 58.0 4.25e-01 80.0% 49.3%
1hr5A00 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 0.79 54.0 5.47e-01 72.0% 75.0%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.78 53.0 5.49e-01 72.0% 76.6%
4x5mA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.78 53.0 4.47e-01 74.0% 41.9%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.77 53.0 4.35e-01 72.0% 41.3%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.76 57.0 5.23e-01 80.0% 62.5%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.76 52.0 3.89e-01 72.0% 40.3%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 51.0 3.68e-01 72.0% 24.8%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.75 52.0 4.40e-01 72.0% 43.4%
1w53A00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.75 64.0 5.46e-01 98.0% 66.7%
3k7xA00 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.75 67.0 3.98e-01 100.0% 50.7%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.74 52.0 4.37e-01 74.0% 45.3%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.74 51.0 3.86e-01 74.0% 40.5%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 54.0 4.86e-01 80.0% 56.5%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.74 55.0 4.87e-01 80.0% 64.8%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.74 51.0 4.35e-01 72.0% 45.1%
1konA01 1.10.10.200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Integrase, N-terminal zinc-binding domain 0.73 57.0 5.20e-01 90.0% 64.7%
1aueB00 1.20.120.150 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain 0.73 60.0 5.00e-01 96.0% 95.7%
2hroA02 1.10.274.10 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › PtsI, HPr-binding domain 0.72 49.0 3.67e-01 72.0% 28.1%
1kaeA03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 49.0 4.83e-01 70.0% 63.6%
1cpyA02 1.10.287.410 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 49.0 4.42e-01 74.0% 50.0%
5djsA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.71 54.0 3.98e-01 86.0% 48.3%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.71 54.0 5.35e-01 84.0% 90.4%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.71 48.0 4.25e-01 72.0% 48.7%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.71 49.0 3.39e-01 74.0% 21.7%
3vtxB00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.71 53.0 3.64e-01 84.0% 23.0%
3ne5B04 6.10.140.730 Special › Helix non-globular › Helix Hairpins › 0.70 57.0 5.73e-01 94.0% 100.0%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.70 57.0 4.44e-01 92.0% 65.5%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 49.0 4.48e-01 74.0% 58.8%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 54.0 5.04e-01 86.0% 82.5%
3vw5A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.70 62.0 3.63e-01 100.0% 52.4%
3beyD00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.70 53.0 4.45e-01 88.0% 47.9%
2bkkC02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.69 59.0 4.12e-01 100.0% 46.8%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.69 48.0 4.06e-01 74.0% 44.8%
4g09A03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 46.0 4.55e-01 72.0% 63.6%
7y4rB01 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.69 56.0 4.52e-01 96.0% 46.2%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 45.0 4.57e-01 70.0% 70.6%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.68 50.0 4.53e-01 84.0% 76.0%
2ouwB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.67 55.0 4.12e-01 96.0% 36.0%
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 0.63 55.0 5.34e-01 98.0% 98.2%
2dsjA01 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 46.0 4.32e-01 98.0% 74.6%
1uouA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.55 43.0 4.08e-01 98.0% 76.5%
3d5lB01 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 45.0 3.69e-01 100.0% 48.0%
4gtnA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.54 43.0 3.96e-01 100.0% 70.3%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.53 40.0 3.86e-01 96.0% 74.6%
1vquA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.53 40.0 3.82e-01 96.0% 73.1%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5016128 3843.1.1.6 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › MrpF_PhaF 0.89 62.0 5.28e-01 72.0% 48.0%
3441654 109.3.1.163 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_2, Ank_4, Ank_5 0.86 57.0 3.38e-01 70.0% 9.9%
3965106 605.1.1.4 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.84 58.0 5.01e-01 72.0% 48.0%
3336677 605.1.1.132 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF641 0.83 57.0 4.97e-01 72.0% 48.0%
3753240 3291.1.1.54 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CC2D1A-B_DM14 0.83 57.0 3.85e-01 72.0% 25.3%
3870171 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.83 56.0 4.96e-01 70.0% 51.4%
3938192 633.22.1.0 alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) 0.82 56.0 3.87e-01 72.0% 31.2%
3451935 192.8.1.359 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF641 0.82 56.0 5.46e-01 72.0% 67.3%
3802185 192.8.1.359 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF641 0.82 56.0 5.01e-01 72.0% 52.9%
3966985 3922.1.1.19 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DUF1090 0.81 56.0 4.35e-01 72.0% 35.6%
4165434 192.6.1.1 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATP-synt_DE 0.81 56.0 5.61e-01 72.0% 74.0%
3666875 1025.1.1.4 alpha bundles › Stonustoxin helical domain › Stonustoxin helical domain › Stonustoxin helical domain › DUF641 0.80 55.0 4.79e-01 72.0% 50.7%
3738041 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.80 55.0 4.58e-01 74.0% 42.4%
3296414 192.29.1.168 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF641 0.79 54.0 4.87e-01 72.0% 52.9%
3542527 5020.1.1.8 extended segments › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › TB2_DP1_HVA22 0.79 54.0 4.52e-01 72.0% 43.5%
3477749 192.1.1.0 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.79 54.0 4.84e-01 74.0% 51.4%
3227443 375.10.1.2 few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha › zf-DPOE 0.79 51.0 4.72e-01 72.0% 53.1%
3375617 192.5.1.30 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › DUF641 0.78 53.0 4.56e-01 72.0% 46.3%
3410968 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.77 52.0 4.72e-01 72.0% 54.3%
5035734 159.1.1.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.76 56.0 4.12e-01 78.0% 45.6%
5001620 632.1.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.76 52.0 4.11e-01 72.0% 34.3%
5025189 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.76 53.0 5.19e-01 74.0% 70.9%
3643501 192.1.1.47 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › DUF641 0.76 53.0 4.91e-01 74.0% 60.0%
3906819 192.17.1.6 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.75 51.0 3.65e-01 72.0% 34.0%
3838463 604.17.1.0 alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.75 57.0 5.72e-01 84.0% 96.0%
3692454 192.1.1.29 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › Es2 0.74 51.0 4.97e-01 72.0% 67.3%
3340500 109.4.1.883 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.73 59.0 3.59e-01 90.0% 15.6%
4066875 7005.1.1.2 a+b duplicates or obligate multimers › LUBAC-tethering domain › LUBAC-tethering domain › LUBAC-tethering domain › LTM 0.73 53.0 5.39e-01 92.0% 82.0%
3965757 159.1.2.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › PRA-PH 0.72 52.0 4.13e-01 78.0% 46.7%
3192999 2003.1.5.120 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Bmt2 0.72 63.0 3.97e-01 100.0% 53.2%
4562960 159.1.2.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › PRA-PH 0.72 52.0 4.10e-01 78.0% 46.7%
3722548 192.6.1.8 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Es2 0.71 48.0 4.81e-01 72.0% 70.0%
3701004 4133.1.1.0 alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like 0.69 59.0 5.06e-01 100.0% 61.2%
5003813 608.1.1.1 alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.69 58.0 5.12e-01 96.0% 66.7%
3806239 616.1.1.0 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.69 60.0 5.25e-01 100.0% 77.3%
3971835 2004.1.1.430 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, ABC_tran_Xtn 0.68 57.0 3.22e-01 94.0% 10.8%
3178367 7524.1.1.2 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Histidinol_dh 0.67 50.0 2.92e-01 82.0% 9.2%
3770274 603.1.1.198 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › DUF4716 0.66 49.0 4.10e-01 84.0% 83.2%
4930318 101.1.4.3 alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3 0.65 53.0 4.09e-01 100.0% 40.0%
4964621 608.1.1.1 alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.64 52.0 4.13e-01 96.0% 42.6%
3081216 109.4.1.17 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin 0.62 50.0 3.94e-01 100.0% 45.2%
4128053 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.56 48.0 4.68e-01 96.0% 89.1%