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RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00493

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00493

Identity

Kingdom:
phage

Quality

88.4 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 7-82
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4jgwA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.78 63.0 4.94e-01 88.2% 50.0%
4fjvA02 1.20.1300.20 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Peptidase C65 Otubain, subdomain 2 0.72 52.0 4.20e-01 76.3% 42.4%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.72 56.0 4.80e-01 82.9% 87.2%
4jgiA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.71 58.0 5.70e-01 88.2% 97.5%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.70 56.0 5.16e-01 85.5% 88.7%
1gpjA01 3.30.460.30 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Glutamyl-tRNA reductase, N-terminal domain 0.68 55.0 4.53e-01 90.8% 66.9%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.67 53.0 3.91e-01 85.5% 87.0%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 50.0 4.55e-01 80.3% 81.2%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.65 51.0 4.69e-01 84.2% 87.8%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.65 50.0 4.57e-01 84.2% 84.5%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.64 53.0 4.66e-01 89.5% 67.3%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.64 54.0 4.83e-01 94.7% 80.9%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 49.0 4.45e-01 84.2% 84.8%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.64 50.0 4.63e-01 85.5% 65.7%
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.64 48.0 4.18e-01 81.6% 78.2%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.64 46.0 4.61e-01 77.6% 93.6%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.64 46.0 4.36e-01 76.3% 95.6%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.63 48.0 4.66e-01 81.6% 83.5%
1vctA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.63 49.0 4.39e-01 85.5% 80.7%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.63 49.0 4.88e-01 84.2% 87.3%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.63 48.0 4.26e-01 84.2% 62.9%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.62 48.0 4.80e-01 85.5% 85.7%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.62 46.0 4.53e-01 80.3% 83.1%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 46.0 4.23e-01 80.3% 84.3%
1e2aA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.60 45.0 4.11e-01 80.3% 84.3%
2mg4A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 41.0 4.29e-01 71.1% 90.9%
3ckyA02 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 0.59 48.0 4.02e-01 89.5% 95.5%
2b8iA00 1.20.1280.100 Mainly Alpha › Up-down Bundle › Monooxygenase › Pas factor, saposin domain 0.59 40.0 4.02e-01 80.3% 68.8%
5n17A01 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.58 41.0 3.79e-01 75.0% 87.5%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.58 44.0 3.98e-01 82.9% 82.2%
1oshA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.58 47.0 3.38e-01 88.2% 66.2%
1fc3B00 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 0.57 40.0 3.72e-01 75.0% 70.3%
1lfuP00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.56 41.0 4.01e-01 76.3% 86.6%
1x0tA01 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 0.56 37.0 4.00e-01 86.8% 85.2%
4k7bA00 1.20.120.1740 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sodium ion translocating NADH-quinone reductase subunit C-like 0.55 42.0 3.76e-01 84.2% 58.6%
1dgnA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.54 34.0 3.27e-01 77.6% 52.8%
4logB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.54 46.0 3.37e-01 100.0% 57.8%
1k74D00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.52 45.0 3.13e-01 98.7% 51.5%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4938696 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.72 57.0 4.66e-01 84.2% 54.8%
5045910 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.72 57.0 4.04e-01 85.5% 35.6%
4623297 109.4.1.70 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CID 0.72 59.0 4.88e-01 90.8% 51.1%
5061845 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.71 54.0 4.94e-01 81.6% 81.0%
4319487 304.41.1.1 ↗ a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.69 58.0 4.59e-01 93.4% 81.9%
3925268 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 54.0 4.93e-01 85.5% 76.0%
3171345 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 53.0 4.04e-01 85.5% 47.2%
3648687 604.12.1.89 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › CDP-OH_P_transf 0.67 52.0 4.88e-01 84.2% 86.3%
3737781 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.66 51.0 4.64e-01 84.2% 80.0%
3427778 604.1.1.144 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF26575 0.66 48.0 4.74e-01 76.3% 92.5%
4646569 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.66 50.0 4.72e-01 82.9% 80.0%
3582234 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.65 51.0 4.65e-01 84.2% 77.0%
3171100 603.1.1.100 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27017 0.65 51.0 4.68e-01 85.5% 90.0%
4015562 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 50.0 4.69e-01 84.2% 68.4%
3271959 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 50.0 4.67e-01 84.2% 81.1%
4018811 603.1.1.158 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › KAR9 0.64 49.0 4.18e-01 84.2% 72.3%
4959083 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 48.0 3.79e-01 84.2% 44.1%
3585899 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.63 49.0 4.36e-01 85.5% 83.6%
4954407 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.62 49.0 4.46e-01 85.5% 73.3%
4012148 604.13.1.0 ↗ alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like 0.62 51.0 4.52e-01 92.1% 73.9%
3186698 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.62 44.0 4.33e-01 75.0% 100.0%
4995144 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 0.61 47.0 3.57e-01 82.9% 76.5%
3573603 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.60 47.0 3.73e-01 85.5% 87.5%
4291115 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.60 50.0 4.98e-01 100.0% 86.3%
3933315 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.59 49.0 4.55e-01 94.7% 89.0%
5040194 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.58 48.0 4.41e-01 90.8% 84.0%
5032080 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.58 44.0 3.95e-01 85.5% 73.0%
4187827 7516.1.1.0 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases 0.52 42.0 2.74e-01 93.4% 91.0%
3594732 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.50 41.0 3.21e-01 90.8% 66.5%
D2 high residues 93-136
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13735.13 best tRNA_NucTran2_2 28.0 2.80e-06 95.5% 27.5%
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2co9A00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.75 52.0 4.04e-01 75.0% 32.4%
1wgfA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.71 49.0 4.67e-01 72.7% 60.4%
1n5uA01 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.70 59.0 4.62e-01 100.0% 51.5%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 47.0 3.84e-01 72.7% 78.5%
2i5uA00 1.10.10.630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DnaD domain-like 0.67 54.0 4.71e-01 100.0% 81.8%
3dd9D02 6.10.140.2060 Special › Helix non-globular › Helix Hairpins › 0.66 49.0 5.01e-01 77.3% 92.7%
6nqiA01 3.30.420.230 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Prp8 RNase H domain, palm region 0.65 51.0 3.56e-01 86.4% 87.2%
3kdgA02 3.30.1370.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › MutL, C-terminal domain, regulatory subdomain 0.64 55.0 4.39e-01 100.0% 61.7%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.64 52.0 3.20e-01 97.7% 46.2%
4zqeA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.64 51.0 4.19e-01 100.0% 65.6%
4wesB03 1.20.89.10 Mainly Alpha › Up-down Bundle › Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 › Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 0.64 43.0 3.59e-01 70.5% 57.0%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.63 44.0 3.69e-01 75.0% 77.0%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.62 53.0 4.28e-01 100.0% 86.4%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 49.0 4.19e-01 100.0% 63.5%
1ysyA00 1.10.8.370 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › nsp7 replicase 0.61 47.0 4.09e-01 100.0% 52.9%
1qguB04 1.20.89.10 Mainly Alpha › Up-down Bundle › Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 › Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 0.54 44.0 3.64e-01 95.5% 56.6%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3620454 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.75 53.0 3.69e-01 77.3% 22.7%
4942992 103.5.1.0 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like 0.73 60.0 5.86e-01 100.0% 88.0%
4973086 103.5.1.0 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like 0.73 62.0 5.86e-01 100.0% 80.0%
3684989 101.26.1.2 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › HTH_44 0.70 54.0 3.82e-01 86.4% 80.0%
4335143 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.69 59.0 4.64e-01 100.0% 57.9%
4305577 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.68 58.0 4.53e-01 100.0% 55.0%
4562076 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.67 57.0 4.38e-01 100.0% 52.4%
3968776 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.59 48.0 2.99e-01 95.5% 52.4%
4339647 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.56 47.0 2.89e-01 97.7% 58.6%
3746492 5059.1.1.34 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA, Nuc_sug_transp 0.55 45.0 2.77e-01 97.7% 58.1%