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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00304

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00304

Identity

Kingdom:
phage

Quality

90.1 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 3-76
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h6pC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.71 36.0 4.16e-01 97.3% 66.1%
1avcA07 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.65 41.0 4.11e-01 100.0% 61.3%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 44.0 3.38e-01 100.0% 29.6%
2qytA02 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 0.62 52.0 4.72e-01 97.3% 70.3%
1u84A00 1.10.340.20 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Apc36109-like domain 0.61 49.0 4.79e-01 93.2% 80.2%
3fhnA02 1.20.58.1420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain B 0.60 50.0 4.39e-01 94.6% 78.6%
1ds8M02 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.60 47.0 3.74e-01 87.8% 39.9%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.59 34.0 3.26e-01 86.5% 48.3%
2c5zA00 1.10.1740.100 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Set2, Rpb1 interacting domain 0.59 41.0 3.86e-01 74.3% 58.1%
3iruA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.59 44.0 4.38e-01 87.8% 78.2%
2qkmB01 1.10.10.1050 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Dcp2, box A domain 0.59 47.0 4.34e-01 91.9% 69.6%
5zzjA02 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.58 46.0 3.10e-01 86.5% 29.9%
3o4yA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.58 50.0 4.40e-01 97.3% 88.2%
1h99A02 1.10.1790.10 Mainly Alpha › Orthogonal Bundle › PTS-regulatory domain, PRD › PRD domain 0.58 47.0 4.24e-01 91.9% 93.4%
2l22A01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.57 45.0 4.21e-01 85.1% 72.5%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.57 51.0 4.48e-01 100.0% 69.1%
1wwiA00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.56 39.0 3.21e-01 74.3% 74.8%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.56 38.0 3.72e-01 75.7% 63.4%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.56 42.0 3.22e-01 81.1% 100.0%
2cgqA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.56 42.0 4.24e-01 82.4% 89.2%
1aa7A02 1.10.10.180 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Influenza matrix protein M1, N-terminal subdomain 2 0.56 37.0 3.72e-01 97.3% 65.4%
4neoA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.55 44.0 4.30e-01 90.5% 84.3%
2nq2A00 1.10.3470.10 Mainly Alpha › Orthogonal Bundle › ABC transporter involved in vitamin B12 uptake, BtuC › ABC transporter involved in vitamin B12 uptake, BtuC 0.55 47.0 3.19e-01 100.0% 72.7%
3kxwA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.55 48.0 4.08e-01 98.6% 72.6%
7qv0F01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.55 44.0 4.29e-01 87.8% 85.2%
4l7aA00 3.40.390.70 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › 0.55 44.0 3.03e-01 86.5% 69.7%
2lkiA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.55 43.0 4.20e-01 85.1% 88.0%
2ktmA00 1.10.790.10 Mainly Alpha › Orthogonal Bundle › Major Prion Protein › Prion/Doppel protein, beta-ribbon domain 0.54 37.0 3.88e-01 71.6% 79.4%
1a41A02 1.20.120.380 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 0.54 46.0 4.33e-01 98.6% 95.7%
1irxA05 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.54 44.0 4.18e-01 93.2% 92.5%
2mr7A00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.54 43.0 4.05e-01 89.2% 73.6%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.53 46.0 4.30e-01 100.0% 86.6%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.53 37.0 3.49e-01 74.3% 95.8%
1zvzA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 38.0 3.29e-01 77.0% 90.3%
4r0mA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 46.0 4.11e-01 98.6% 88.0%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 36.0 3.71e-01 82.4% 73.6%
1i5nB00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.53 38.0 3.25e-01 77.0% 62.9%
3hdiA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 41.0 3.17e-01 91.9% 72.2%
1ldjA04 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.52 41.0 3.55e-01 100.0% 54.8%
3mzoB00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.52 43.0 3.28e-01 100.0% 43.3%
4h0cA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 42.0 3.09e-01 91.9% 68.1%
1ldjA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.51 45.0 3.82e-01 100.0% 66.4%
2ptfB02 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.51 35.0 3.86e-01 81.1% 93.0%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4110524 4979.2.1.1 ↗ alpha arrays › C-terminal domain of Hypothetical protein MPN330-like › XRN2-binding domain (XTBD) › XRN2-binding domain (XTBD) › XTBD 0.72 50.0 4.58e-01 71.6% 57.9%
3623551 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.71 54.0 3.97e-01 81.1% 71.1%
3586132 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 0.67 60.0 5.54e-01 100.0% 77.9%
3515847 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 0.66 59.0 5.45e-01 100.0% 81.1%
4025289 192.29.1.197 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF4110 0.66 45.0 4.38e-01 78.4% 62.4%
3666802 101.1.2.518 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_DNAJC9 0.66 47.0 4.25e-01 100.0% 55.0%
3389549 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 0.66 58.0 5.49e-01 98.6% 82.2%
3811948 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.66 45.0 4.65e-01 70.3% 80.0%
3224103 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 58.0 4.86e-01 98.6% 95.2%
3294610 109.4.1.459 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › eIF3_p135 0.64 56.0 4.55e-01 100.0% 76.6%
3309361 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 0.62 53.0 4.66e-01 100.0% 63.0%
3832740 3567.1.1.16 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › DUF4110 0.62 46.0 4.33e-01 78.4% 67.8%
3654210 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 0.62 52.0 5.20e-01 97.3% 98.7%
3468538 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 55.0 4.54e-01 98.6% 56.9%
1174232 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 0.62 52.0 5.27e-01 97.3% 100.0%
3989247 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.61 50.0 4.42e-01 90.5% 87.3%
3406182 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.61 53.0 4.73e-01 100.0% 94.5%
3412670 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.61 52.0 3.39e-01 98.6% 72.1%
4016091 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.61 43.0 4.16e-01 74.3% 92.9%
3877341 109.4.1.87 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec6 0.60 55.0 3.98e-01 100.0% 40.5%
2580914 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.60 48.0 4.24e-01 87.8% 69.4%
4015733 132.1.1.0 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) 0.60 49.0 4.41e-01 90.5% 68.0%
3209602 5042.1.1.0 ↗ extended segments › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region 0.60 40.0 4.04e-01 75.7% 68.0%
3228866 101.6.1.0 ↗ alpha arrays › HTH › Protein serine/threonine phosphatase 2C-C › Protein serine/threonine phosphatase 2C-C 0.60 52.0 5.11e-01 100.0% 92.5%
3588554 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.60 47.0 4.21e-01 86.5% 91.4%
4172555 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.59 52.0 4.59e-01 94.6% 98.1%
3508184 101.1.2.103 ↗ alpha arrays › HTH › HTH › winged helix domain › SelB-wing_2 0.59 51.0 5.15e-01 100.0% 96.0%
3731037 109.24.1.4 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in dedicator of cytokinesis protein 9 › Helical domain in dedicator of cytokinesis protein 9 › XPG_I_2 0.58 50.0 3.64e-01 100.0% 58.7%
4593785 132.1.1.0 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) 0.58 46.0 4.28e-01 89.2% 78.9%
3707374 109.4.1.1341 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG3_N, COG3_C 0.58 51.0 3.06e-01 100.0% 15.7%
149829 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.58 47.0 4.16e-01 91.9% 85.0%
3317357 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.58 36.0 2.53e-01 82.4% 20.0%
4928215 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.58 49.0 4.62e-01 98.6% 92.6%
3739207 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.57 48.0 4.52e-01 97.3% 100.0%
4564250 103.1.1.67 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › UPF0515 0.57 52.0 4.90e-01 100.0% 93.3%
5037670 604.39.1.0 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters 0.57 47.0 3.68e-01 94.6% 70.9%
3277050 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.56 44.0 4.30e-01 87.8% 82.4%
4060837 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.56 39.0 2.79e-01 74.3% 71.8%
5064355 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.56 46.0 4.46e-01 100.0% 96.7%
5052887 604.4.1.0 ↗ alpha bundles › Spectrin repeat-like › Alpha-hemoglobin stabilizing protein AHSP › Alpha-hemoglobin stabilizing protein AHSP 0.56 46.0 4.56e-01 91.9% 88.7%
3520337 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.56 48.0 4.23e-01 98.6% 98.3%
5055207 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.56 40.0 3.87e-01 75.7% 75.3%
3346388 180.1.1.1 ↗ alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2 0.56 49.0 3.62e-01 100.0% 42.5%
3771911 109.4.1.1512 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Tcp11 0.55 45.0 3.41e-01 90.5% 41.6%
3365302 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 38.0 2.61e-01 89.2% 19.3%
3488368 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.54 44.0 4.38e-01 89.2% 89.9%
4612393 7579.1.1.234 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DUF6792 0.54 45.0 3.10e-01 93.2% 50.0%
3346653 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.54 40.0 3.58e-01 79.7% 76.2%
4624369 5069.1.1.15 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.53 40.0 3.29e-01 82.4% 93.8%
3955584 191.1.1.48 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_46 0.53 45.0 3.66e-01 100.0% 54.2%
5061121 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.52 41.0 4.08e-01 86.5% 86.7%
4027154 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 0.51 44.0 3.97e-01 94.6% 81.0%
3465231 192.15.1.189 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Frigida 0.50 36.0 3.59e-01 77.0% 82.5%
3172661 5069.1.3.108 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › PF30349 0.50 35.0 3.28e-01 75.7% 58.9%