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RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00342

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00342

Identity

Kingdom:
phage

Quality

82.4 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 7-79
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4hb9A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 44.0 2.84e-01 100.0% 48.3%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4139864 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.69 47.0 4.31e-01 71.2% 64.3%
3531032 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 48.0 3.30e-01 76.7% 25.4%
3417244 220.1.1.64 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C1_MyoVII 0.64 39.0 3.63e-01 100.0% 47.4%
4026519 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.62 47.0 3.90e-01 82.2% 96.3%
4067487 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.62 43.0 3.98e-01 74.0% 98.9%
3939128 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 41.0 3.61e-01 100.0% 47.3%
3283274 2002.1.1.152 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_3 0.55 42.0 2.54e-01 82.2% 94.2%
5031053 244.4.1.2 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › NiFeSe_Hases 0.54 38.0 3.75e-01 98.6% 68.8%
5022868 244.4.1.2 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › NiFeSe_Hases 0.52 37.0 3.51e-01 90.4% 62.5%
D2 high residues 90-140
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1b8bA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.85 63.0 3.53e-01 80.4% 7.5%
1ldjA02 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.80 54.0 4.03e-01 70.6% 29.3%
3fnnA03 6.10.140.440 Special › Helix non-globular › Helix Hairpins › 0.80 55.0 5.97e-01 72.5% 88.4%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.80 71.0 4.75e-01 98.0% 36.2%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 54.0 4.29e-01 70.6% 53.1%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 52.0 5.30e-01 70.6% 70.6%
3x0uB01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.76 57.0 3.62e-01 80.4% 32.1%
2ktmA00 1.10.790.10 Mainly Alpha › Orthogonal Bundle › Major Prion Protein › Prion/Doppel protein, beta-ribbon domain 0.75 55.0 4.98e-01 78.4% 64.7%
4nxiA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.75 60.0 4.09e-01 100.0% 24.4%
2qgsB01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.74 63.0 5.35e-01 100.0% 56.8%
3ktcA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.74 51.0 3.08e-01 88.2% 11.2%
1sg7A00 1.10.1740.70 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › ChaB 0.74 66.0 5.77e-01 100.0% 78.7%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.73 64.0 5.63e-01 100.0% 73.7%
4bkxA01 4.10.1240.50 Few Secondary Structures › Irregular › Hormone receptor fold › 0.73 53.0 4.11e-01 78.4% 37.2%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.73 51.0 4.68e-01 72.5% 62.5%
1ls1A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.72 62.0 5.22e-01 98.0% 88.8%
2no4A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.72 62.0 5.49e-01 98.0% 72.0%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.72 59.0 5.15e-01 100.0% 60.5%
3v53E00 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.70 48.0 3.85e-01 72.5% 36.3%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.70 55.0 4.47e-01 84.3% 66.3%
4tq1A03 1.10.246.190 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Autophagy protein Apg5, helix rich domain 0.69 49.0 4.71e-01 74.5% 72.4%
4mk6A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.69 60.0 4.08e-01 100.0% 34.0%
3anwA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 54.0 4.16e-01 86.3% 61.1%
3fd0A01 3.90.1150.60 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Methioning gamme-lyase, C-terminal domain 0.68 53.0 3.55e-01 84.3% 77.2%
2ffjA02 1.10.285.20 Mainly Alpha › Orthogonal Bundle › Glutamate Dehydrogenase; Chain A, domain 3 › Uncharacterised protein PF01937, DUF89, domain 2 0.68 50.0 4.70e-01 100.0% 64.6%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.67 51.0 4.43e-01 84.3% 59.8%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 47.0 4.27e-01 74.5% 57.7%
5kdiA00 1.10.3520.10 Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein 0.67 59.0 3.86e-01 98.0% 45.0%
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 0.66 56.0 4.42e-01 100.0% 44.1%
3u4qA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 48.0 3.15e-01 78.4% 18.0%
3toyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.66 45.0 3.41e-01 70.6% 29.1%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.66 50.0 4.37e-01 86.3% 65.1%
4kjmB01 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 0.65 54.0 5.08e-01 100.0% 74.6%
3ermB00 1.10.10.710 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › PSPTO_1197 like 0.64 46.0 4.37e-01 80.4% 68.8%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.63 51.0 3.95e-01 90.2% 49.6%
3iv7A02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.62 54.0 3.62e-01 100.0% 28.6%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.62 49.0 4.22e-01 100.0% 54.3%
1v4gA01 6.10.140.800 Special › Helix non-globular › Helix Hairpins › 0.61 44.0 4.03e-01 80.4% 58.0%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 53.0 4.68e-01 100.0% 66.7%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.58 50.0 3.80e-01 100.0% 61.1%
3pfyA02 6.10.20.180 Special › Helix non-globular › Arc Repressor Mutant, subunit A › 0.56 47.0 4.58e-01 94.1% 93.0%
3ddmA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.41e-01 100.0% 46.4%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4940884 3542.1.1.2 ↗ alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › SPP 0.92 71.0 4.26e-01 80.4% 15.4%
3986989 5054.1.1.68 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › AI-2E_transport 0.90 66.0 4.46e-01 78.4% 24.7%
3978395 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.88 65.0 3.61e-01 80.4% 6.6%
3949156 2500.1.1.7 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Gly_radical, NRDD 0.88 65.0 3.61e-01 80.4% 6.6%
4540106 3396.1.1.3 ↗ extended segments › HIG1 domain family member 1A › HIG1 domain family member 1A › HIG1 domain family member 1A › DUF4481 0.87 66.0 5.55e-01 80.4% 57.5%
3974187 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.86 64.0 5.20e-01 78.4% 46.7%
4483958 6155.2.1.1 ↗ alpha duplicates or obligate multimers › TOG superfamily › PnuC › PnuC › NMN_transporter 0.85 62.0 3.92e-01 78.4% 17.6%
3741742 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.82 68.0 4.23e-01 90.2% 46.0%
3609311 7575.1.1.0 ↗ a/b three-layered sandwiches › Caspase-like › Caspase-like › Caspase-like 0.82 71.0 4.76e-01 100.0% 26.5%
3781725 3291.1.1.12 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › DUF1689 0.81 61.0 4.50e-01 80.4% 37.6%
7384 219.1.1.21 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C58 0.80 71.0 4.75e-01 98.0% 36.2%
3456717 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.79 52.0 4.80e-01 72.5% 53.8%
4569740 3860.1.1.1 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm › IQ 0.79 57.0 4.48e-01 78.4% 38.2%
3921797 5049.1.2.1 ↗ alpha complex topology › Ammonium transporter-related › Ammonium transporter-related › Urea transporter › UT 0.78 68.0 4.10e-01 100.0% 18.9%
4004120 1075.5.1.5 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Rft-1 0.78 67.0 3.96e-01 100.0% 15.4%
5040031 632.22.1.199 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › PLDc_N 0.78 67.0 5.72e-01 100.0% 77.6%
3833662 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.77 64.0 3.87e-01 90.2% 42.3%
4999592 103.4.1.0 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.77 68.0 6.00e-01 100.0% 81.3%
3263943 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.77 60.0 3.58e-01 84.3% 33.6%
3648996 605.1.1.173 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › PF28744 0.77 55.0 4.56e-01 76.5% 44.4%
3398509 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.74 66.0 4.02e-01 98.0% 71.0%
3276564 5043.1.1.22 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › PigN 0.74 56.0 3.77e-01 80.4% 23.8%
4928060 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.74 54.0 4.30e-01 80.4% 41.3%
3575 4084.1.1.1 ↗ alpha bundles › ChaB-like › ChaB-like › ChaB-like › ChaB 0.74 66.0 5.77e-01 100.0% 78.7%
3573570 604.33.1.0 ↗ alpha bundles › Spectrin repeat-like › Repulsive guidance molecule (RGM) N-terminal domain › Repulsive guidance molecule (RGM) N-terminal domain 0.73 55.0 4.54e-01 82.4% 49.5%
5043090 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.73 55.0 4.72e-01 80.4% 57.5%
4021030 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.73 56.0 3.81e-01 82.4% 23.2%
3323416 3831.1.1.7 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › DUF842 0.72 61.0 4.95e-01 100.0% 74.3%
4995832 5076.2.1.13 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › DUF7847 0.72 53.0 3.36e-01 80.4% 16.8%
5074875 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.71 60.0 5.08e-01 98.0% 86.7%
3631283 5069.1.1.82 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › PigN 0.71 58.0 3.88e-01 90.2% 55.4%
4028766 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.70 57.0 4.95e-01 100.0% 58.9%
5078048 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 0.70 47.0 4.16e-01 70.6% 64.0%
3926812 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.70 62.0 5.61e-01 100.0% 87.1%
5027220 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.69 51.0 4.87e-01 80.4% 71.7%
3599328 616.1.1.6 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Mpo1-like 0.69 55.0 4.55e-01 84.3% 51.1%
3726873 601.1.2.108 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › PigN 0.69 55.0 3.76e-01 88.2% 57.8%
1120983 103.9.1.1 ↗ alpha arrays › RuvA-C › RanGAP2 N-terminal domain › RanGAP2 N-terminal domain › WPP 0.68 58.0 5.69e-01 96.1% 98.2%
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 0.61 54.0 3.73e-01 100.0% 30.0%