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SRR1747018_scaffold_15_prodigal-single.1__X__X__00103

Bact-Vir

SRR1747018_scaffold_15_prodigal-single.1__X__X__00103

Identity

Kingdom:
phage

Quality

86.0 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 medium residues 1-119
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00882.25 best Zn_dep_PLPC 56.1 6.40e-15 96.6% 72.6%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ah7A00 1.10.575.10 Mainly Alpha › Orthogonal Bundle › P1 Nuclease › P1 Nuclease 0.83 78.0 6.03e-01 100.0% 66.1%
3c18A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.63 37.0 3.78e-01 96.6% 58.5%
3p9dG01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.58 52.0 4.06e-01 99.2% 94.5%
2c0gA02 1.20.1150.12 Mainly Alpha › Up-down Bundle › Endoplasmic reticulum protein erp29 › Endoplasmic reticulum resident protein 29, C-terminal domain 0.53 40.0 4.19e-01 77.3% 95.3%
6k6iA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 46.0 3.80e-01 99.2% 65.8%
6lcuA02 1.10.10.470 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Maltooligosyl trehalose synthase; domain 4 0.51 36.0 3.83e-01 82.4% 82.9%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.50 35.0 4.02e-01 78.2% 100.0%
7p5hB03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.50 36.0 4.06e-01 77.3% 100.0%
4a5dB00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.50 37.0 2.99e-01 76.5% 65.9%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5055797 177.1.1.0 ↗ alpha bundles › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease 0.76 70.0 5.90e-01 100.0% 93.2%
3235302 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.72 35.0 2.71e-01 78.2% 22.4%
5067364 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 0.70 56.0 4.60e-01 84.0% 57.6%
4938457 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 0.65 51.0 4.10e-01 84.0% 54.0%
3909442 3236.1.1.1 ↗ alpha complex topology › Cation-proton antiporter › Cation-proton antiporter (CPA) › Cation-proton antiporter (CPA) › Na_H_Exchanger 0.64 51.0 3.42e-01 86.6% 36.0%
3187211 592.1.1.2 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.59 37.0 3.76e-01 83.2% 62.5%
3465983 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 0.57 45.0 4.36e-01 86.6% 92.9%
3346956 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.57 38.0 4.26e-01 74.8% 86.3%
3860132 109.4.1.176 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cnd1,Cnd1_N 0.57 41.0 2.34e-01 74.8% 19.0%
5077421 180.1.1.0 ↗ alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase 0.55 49.0 4.25e-01 100.0% 88.2%
3182141 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 0.53 46.0 3.84e-01 99.2% 60.4%
3415190 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 0.53 46.0 3.94e-01 99.2% 69.3%
3734078 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 0.53 45.0 3.78e-01 98.3% 60.4%
3994626 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 0.53 43.0 3.67e-01 93.3% 66.4%
3827460 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.52 40.0 3.62e-01 81.5% 90.3%
3711714 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 37.0 2.82e-01 75.6% 51.3%
4939433 5079.1.1.1 ↗ alpha duplicates or obligate multimers › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › MgtE 0.50 41.0 3.46e-01 91.6% 69.5%
4941726 5079.1.1.1 ↗ alpha duplicates or obligate multimers › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › MgtE 0.50 41.0 3.46e-01 91.6% 70.9%
3277239 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 37.0 3.24e-01 77.3% 69.1%
D2 medium residues 120-207
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vm6A00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.71 52.0 4.44e-01 96.6% 47.9%
7eu3E01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 51.0 5.19e-01 87.5% 77.0%
1c17M00 1.20.120.220 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ATP synthase, F0 complex, subunit A 0.69 62.0 5.27e-01 98.9% 69.0%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 48.0 5.08e-01 73.9% 85.9%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.66 46.0 4.98e-01 72.7% 89.2%
5af7B03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.65 48.0 4.03e-01 77.3% 57.4%
1ungE00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.63 38.0 3.21e-01 84.1% 35.4%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.63 51.0 4.84e-01 88.6% 74.5%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.62 43.0 4.42e-01 71.6% 85.4%
3l09A01 1.20.58.1460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 4.31e-01 90.9% 67.3%
1wleA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.60 43.0 3.96e-01 75.0% 61.4%
4rfsS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.60 53.0 4.20e-01 100.0% 80.7%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.58 46.0 4.63e-01 95.5% 85.2%
1tt5C01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 45.0 3.05e-01 100.0% 22.9%
1j1jA01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.55 45.0 4.06e-01 95.5% 62.1%
1a7vA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.55 45.0 4.03e-01 90.9% 76.8%
1iq0A03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.55 47.0 4.33e-01 96.6% 79.3%
1xdxA01 3.30.1140.40 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 0.55 50.0 4.77e-01 100.0% 91.0%
2lsgA00 1.20.58.1280 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DNA repair protein Rev1, C-terminal domain 0.54 37.0 3.63e-01 94.3% 63.9%
1zvzA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 46.0 4.20e-01 97.7% 80.6%
1s35A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 46.0 4.32e-01 95.5% 84.5%
1u5pA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 45.0 4.30e-01 95.5% 86.1%
1hciA04 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 45.0 4.16e-01 97.7% 80.7%
7kdfB01 1.10.418.60 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Ncd80 complex, Nuf2 subunit 0.52 39.0 3.32e-01 79.5% 67.8%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.50 41.0 4.11e-01 96.6% 86.0%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3386308 604.3.1.46 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › PF28048 0.74 57.0 5.73e-01 100.0% 80.0%
3486453 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.72 63.0 5.96e-01 96.6% 85.7%
3259377 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.69 58.0 5.70e-01 100.0% 86.3%
3919099 621.1.1.8 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › GVIN1 0.68 60.0 5.24e-01 98.9% 80.0%
4027155 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.68 53.0 5.60e-01 100.0% 100.0%
4537299 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.68 59.0 3.89e-01 98.9% 22.3%
3743047 604.5.1.28 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › TBCC_N 0.67 54.0 5.50e-01 96.6% 90.6%
4176201 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.66 57.0 5.57e-01 100.0% 89.5%
3616157 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.64 57.0 5.56e-01 97.7% 90.5%
4594465 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 0.64 50.0 4.96e-01 100.0% 80.0%
4594071 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 0.64 50.0 5.06e-01 100.0% 88.2%
5054557 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.63 53.0 5.27e-01 94.3% 88.9%
5019542 622.4.1.67 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › DUF5518 0.63 54.0 5.29e-01 98.9% 91.9%
5076586 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 53.0 5.20e-01 95.5% 90.8%
3744146 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.62 50.0 5.05e-01 95.5% 87.8%
5055943 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 52.0 5.06e-01 95.5% 83.0%
4674952 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 0.62 51.0 4.93e-01 100.0% 81.0%
3403421 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 43.0 3.64e-01 97.7% 43.2%
3681880 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 0.60 47.0 4.10e-01 98.9% 54.8%
3794203 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.60 44.0 4.46e-01 100.0% 81.2%
3739620 168.1.1.1 ↗ alpha arrays › Sec7 domain › Sec7 domain › Sec7 domain › Sec7 0.59 51.0 3.89e-01 100.0% 59.6%
3567382 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 49.0 4.58e-01 95.5% 86.1%
5030379 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.58 39.0 3.95e-01 72.7% 68.9%
3402040 108.2.1.0 ↗ alpha arrays › EF-hand › Insect pheromone/odorant-binding proteins › Insect pheromone/odorant-binding proteins 0.58 47.0 3.84e-01 87.5% 76.2%
4527464 633.24.1.5 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › PF29080 0.58 49.0 4.81e-01 100.0% 88.4%
3917085 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 47.0 4.61e-01 95.5% 86.3%
4992256 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 48.0 4.67e-01 95.5% 86.9%
3491815 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.56 45.0 4.45e-01 95.5% 83.0%
4320989 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.55 45.0 4.07e-01 89.8% 81.7%
3221766 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 46.0 4.40e-01 97.7% 80.0%
3800823 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 47.0 4.43e-01 97.7% 81.0%
3792010 604.1.1.105 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_Anc-1_2 0.54 45.0 4.33e-01 95.5% 80.0%
3585628 109.3.1.170 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_4 0.53 42.0 3.12e-01 92.0% 32.2%
3587045 5065.1.1.2 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › FecCD 0.50 43.0 3.06e-01 100.0% 55.0%