←Back to structures

S2_009_000_R2_scaffold_26_prodigal-single.1__X__X__00395

Bact-Vir

S2_009_000_R2_scaffold_26_prodigal-single.1__X__X__00395

Identity

Kingdom:
phage

Quality

76.9 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 5-76
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fioA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 58.0 4.12e-01 81.9% 47.4%
2cmrA00 1.20.58.1860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 59.0 4.24e-01 86.1% 85.9%
2i9cA01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.72 59.0 5.08e-01 87.5% 57.7%
1za0A00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.71 58.0 3.94e-01 87.5% 43.8%
4g10A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.70 55.0 4.46e-01 84.7% 83.1%
3ea5D00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.69 52.0 2.91e-01 80.6% 13.5%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 47.0 4.21e-01 70.8% 83.8%
1fewA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 54.0 4.04e-01 84.7% 64.7%
5ux1D00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 59.0 4.22e-01 94.4% 37.6%
6humG01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.67 51.0 3.82e-01 79.2% 60.0%
4hfkB00 1.20.120.1620 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.66 61.0 5.46e-01 100.0% 83.7%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.66 60.0 4.37e-01 100.0% 55.6%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.66 52.0 4.56e-01 83.3% 74.5%
1o5hA00 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.66 52.0 3.69e-01 83.3% 38.5%
6p6jB01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.65 55.0 3.55e-01 91.7% 81.2%
3rkoF01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.63 52.0 3.91e-01 86.1% 64.4%
8anqA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.63 52.0 3.55e-01 86.1% 45.1%
4hhxA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.63 56.0 5.01e-01 100.0% 91.3%
4hz4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 49.0 4.20e-01 83.3% 61.6%
1vw4L01 3.90.1030.10 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 0.62 53.0 4.21e-01 100.0% 48.1%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.62 52.0 3.89e-01 90.3% 37.6%
3c5wA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.62 43.0 3.02e-01 83.3% 22.8%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.62 46.0 3.86e-01 80.6% 92.1%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.62 54.0 3.89e-01 93.1% 49.7%
3rm5B02 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.61 48.0 3.43e-01 87.5% 37.9%
1zs3A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.60 50.0 3.81e-01 100.0% 39.2%
6vvoE02 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.59 41.0 3.75e-01 86.1% 53.5%
1xeqB00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.58 50.0 4.74e-01 100.0% 81.2%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.57 53.0 4.33e-01 100.0% 80.2%
2rd3D00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.57 50.0 3.58e-01 100.0% 82.1%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.55 47.0 4.52e-01 97.2% 83.5%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.55 47.0 4.07e-01 97.2% 94.0%
4lqxA00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.55 42.0 2.83e-01 83.3% 55.4%
4didB01 1.20.58.450 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cell division control protein 42 homolog 0.54 45.0 3.83e-01 90.3% 83.3%
3q23A04 6.10.140.1370 Special › Helix non-globular › Helix Hairpins › 0.52 36.0 3.37e-01 95.8% 57.1%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.52 43.0 2.80e-01 100.0% 64.4%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.51 36.0 3.55e-01 75.0% 74.7%
1xioA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.51 42.0 3.16e-01 100.0% 80.6%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3502309 109.4.1.163 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SYMPK_PTA1_N 0.77 54.0 3.46e-01 81.9% 16.6%
3588719 564.1.1.0 ↗ alpha arrays › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors 0.75 56.0 5.85e-01 86.1% 86.2%
3791 603.1.1.1 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin 0.74 58.0 4.12e-01 81.9% 47.4%
3167993 603.1.1.97 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin, SNARE 0.74 58.0 3.97e-01 81.9% 40.9%
3178557 109.4.1.22 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N 0.72 49.0 3.02e-01 83.3% 12.3%
3744696 603.1.1.2 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Not3 0.70 55.0 4.76e-01 81.9% 72.4%
3918098 604.6.1.57 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › Not3 0.70 55.0 4.78e-01 81.9% 72.4%
3688828 604.10.1.0 ↗ alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac 0.70 54.0 5.48e-01 80.6% 100.0%
4939044 109.4.1.207 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_2 0.69 44.0 3.52e-01 80.6% 34.1%
3832769 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 54.0 4.07e-01 81.9% 50.3%
3647305 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.68 48.0 3.94e-01 81.9% 39.3%
3298596 5050.1.1.33 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_5 0.68 63.0 5.16e-01 100.0% 92.8%
3573718 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.67 60.0 4.26e-01 100.0% 49.1%
3317539 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 52.0 4.40e-01 81.9% 67.8%
4979111 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.67 52.0 4.63e-01 81.9% 75.0%
3465357 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 52.0 4.37e-01 81.9% 69.6%
3811048 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.66 59.0 4.33e-01 97.2% 93.0%
4949390 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.66 60.0 4.41e-01 100.0% 55.7%
185784 3368.1.1.1 ↗ alpha bundles › Rap2b (SMA2266) › Rap2b (SMA2266) › Rap2b (SMA2266) › Tai4 0.66 61.0 5.46e-01 100.0% 83.7%
3733608 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.64 56.0 3.22e-01 97.2% 46.8%
3317090 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.64 57.0 3.88e-01 100.0% 62.7%
3373578 109.4.1.163 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SYMPK_PTA1_N 0.64 48.0 3.60e-01 80.6% 40.0%
3602572 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.63 48.0 3.93e-01 84.7% 62.5%
3724315 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 57.0 4.38e-01 97.2% 82.7%
4989825 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.62 54.0 4.03e-01 100.0% 53.8%
3899601 377.1.1.18 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-AD 0.61 50.0 4.12e-01 88.9% 60.8%
3241687 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.61 47.0 4.01e-01 81.9% 71.3%
3978041 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.61 48.0 3.49e-01 86.1% 70.2%
5062416 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.60 53.0 3.83e-01 98.6% 51.7%
3668287 601.2.1.5 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › Ctr 0.60 52.0 4.50e-01 94.4% 65.5%
3484694 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.60 48.0 3.20e-01 91.7% 91.2%
3881582 310.2.1.31 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › DUF4455 0.60 46.0 4.04e-01 81.9% 87.6%
5080292 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.59 52.0 3.66e-01 97.2% 55.5%
3584182 604.9.1.18 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Zip 0.58 47.0 4.48e-01 88.9% 89.4%
5010730 150.1.2.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase › TENA_THI-4 0.58 44.0 3.26e-01 86.1% 37.2%
3720823 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.57 48.0 2.81e-01 100.0% 12.4%
4065783 150.1.2.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase › TENA_THI-4 0.56 48.0 3.38e-01 95.8% 34.5%
2884853 5000.4.1.1 ↗ alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain › Endotoxin_N 0.55 43.0 3.16e-01 90.3% 92.3%
5041194 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.54 42.0 3.46e-01 90.3% 95.5%
4081378 5067.1.1.2 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › SecD_SecF 0.53 38.0 2.82e-01 79.2% 65.0%
4385935 5000.4.1.1 ↗ alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain › Endotoxin_N 0.51 40.0 2.83e-01 88.9% 82.0%
D2 high residues 88-196
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5dikA00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.63 41.0 4.12e-01 83.5% 64.3%
2oarB00 1.10.1200.120 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Large-conductance mechanosensitive channel, MscL; domain 1 0.58 37.0 3.56e-01 86.2% 56.0%
2zihC00 1.10.3630.10 Mainly Alpha › Orthogonal Bundle › yeast vps74-n-term truncation variant fold › yeast vps74-n-term truncation variant domain like 0.56 44.0 3.36e-01 85.3% 75.6%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.56 36.0 3.84e-01 95.4% 76.1%
2lu1A00 3.30.70.2370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 34.0 3.68e-01 86.2% 73.0%
2af7D00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.55 39.0 3.86e-01 76.1% 90.9%
1zunB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 44.0 3.66e-01 90.8% 66.7%
4udsA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 38.0 3.27e-01 76.1% 83.2%
1neiA00 3.30.160.220 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YoaG 0.52 22.0 2.94e-01 96.3% 73.3%
3e8oB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.78e-01 100.0% 81.0%
6kbyA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 40.0 2.79e-01 85.3% 98.3%
4nohA01 3.30.70.3060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 30.0 3.52e-01 97.2% 90.1%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3326759 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.56 33.0 3.81e-01 75.2% 82.7%
3549652 109.26.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Nuclear pore complex component Nup133/Nup170/Nup157 C-terminal domains › Nuclear pore complex component Nup133/Nup170/Nup157 C-terminal domains › Nucleoporin_C 0.56 43.0 2.60e-01 83.5% 15.0%
4967840 140.1.1.0 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.53 40.0 3.27e-01 78.9% 77.5%
3178578 6166.1.1.1 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › ERG4_ERG24 0.52 40.0 3.30e-01 82.6% 65.9%
4933933 131.1.1.3 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.52 43.0 3.38e-01 91.7% 55.1%
4575479 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.52 45.0 3.07e-01 100.0% 50.6%
4955493 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.51 46.0 3.56e-01 100.0% 71.8%
3712615 6166.1.1.1 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › ERG4_ERG24 0.51 41.0 3.29e-01 86.2% 67.3%