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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00134

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00134

Identity

Kingdom:
phage

Quality

53.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 1-60
PDB
D2 medium residues 88-193
PDB
D3 medium residues 383-489
PDB
Domain cluster: rep: LacPavin_0818_WC55_scaffold_56344_prodigal-single.1__X__X__00173__D343-473
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rn7A01 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 0.75 38.0 4.83e-01 100.0% 81.8%
2y1hB00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.60 39.0 2.88e-01 75.7% 26.4%
3mpiA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.60 42.0 4.12e-01 74.8% 91.7%
3gg7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.59 39.0 2.92e-01 76.6% 29.2%
4ix7A00 1.10.10.2590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › BEN domain 0.58 45.0 4.43e-01 82.2% 87.7%
6l25A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.57 39.0 2.91e-01 75.7% 29.4%
1yixA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.57 39.0 2.90e-01 76.6% 28.3%
1j6oA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.57 39.0 2.88e-01 75.7% 28.8%
2hg2A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.56 50.0 3.72e-01 100.0% 69.9%
1vjxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.56 40.0 3.63e-01 75.7% 75.2%
2xioA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.55 39.0 2.84e-01 73.8% 33.1%
2hujA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.55 38.0 3.64e-01 71.0% 86.4%
5vbfA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.55 48.0 3.60e-01 100.0% 62.8%
1xwyA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.54 39.0 2.90e-01 76.6% 30.8%
2pmiB00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.54 47.0 3.76e-01 100.0% 47.9%
3rk6A00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 36.0 2.89e-01 71.0% 34.6%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.52 35.0 3.96e-01 72.0% 92.4%
3pjaJ01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.52 37.0 3.49e-01 72.9% 73.3%
3h4cA02 1.10.472.110 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › 0.52 43.0 4.29e-01 88.8% 85.5%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.51 40.0 3.82e-01 85.0% 88.9%
3fymA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.51 36.0 3.90e-01 96.3% 96.3%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.50 35.0 3.39e-01 72.9% 73.6%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046381 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.61 39.0 2.95e-01 75.7% 27.6%
4984052 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.60 39.0 2.93e-01 76.6% 28.2%
4978190 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.59 39.0 2.86e-01 75.7% 27.3%
2627935 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.57 39.0 2.91e-01 75.7% 29.4%
3584038 5050.1.1.11 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › UNC-93 0.56 40.0 3.00e-01 72.9% 71.0%
3594739 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.56 40.0 3.02e-01 73.8% 45.3%
3420023 633.21.1.18 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom 0.55 40.0 3.53e-01 77.6% 69.7%
3177836 633.23.1.22 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › MARVEL 0.54 39.0 3.33e-01 75.7% 71.9%
4586750 7524.1.1.1 ↗ a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.54 49.0 3.81e-01 100.0% 84.7%
4019831 5050.1.1.56 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr, TRI12 0.53 37.0 2.47e-01 70.1% 69.3%
5049565 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.53 38.0 2.75e-01 72.9% 33.1%
4646512 633.6.1.3 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › HpaB 0.53 39.0 3.19e-01 79.4% 67.7%
3707503 101.1.10.20 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB_C_2 0.53 44.0 4.19e-01 88.8% 88.8%
3732352 601.39.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › Enhancer of filamentation 1 › Enhancer of filamentation 1 › DUF3433 0.53 37.0 3.15e-01 72.0% 80.6%
3446238 5069.1.1.21 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › DUF2301 0.51 37.0 3.03e-01 75.7% 78.1%
D4 medium residues 490-558
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5j3uA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 46.0 3.79e-01 76.8% 91.9%
4myjA04 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 45.0 3.67e-01 82.6% 86.0%
4nxtA01 1.10.1410.40 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.56 46.0 3.67e-01 91.3% 67.6%
4n30A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 45.0 3.41e-01 91.3% 95.1%
6kzdA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.55 41.0 3.11e-01 82.6% 58.9%
1qoyA00 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.54 40.0 2.68e-01 81.2% 20.5%
6ks6A02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.53 36.0 3.18e-01 81.2% 45.4%
2o7gA00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 41.0 3.89e-01 88.4% 78.4%
6fdmA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.52 36.0 3.10e-01 73.9% 62.7%
2wtvA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.51 41.0 3.13e-01 89.9% 70.6%
4uobA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.51 37.0 3.03e-01 76.8% 45.2%
4c0zA02 1.10.150.480 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.50 37.0 3.37e-01 89.9% 57.3%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.50 35.0 3.58e-01 72.5% 86.4%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3179147 376.1.6.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain › IBR 0.64 45.0 4.19e-01 78.3% 60.0%
3895727 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.60 40.0 4.56e-01 73.9% 96.0%
3264997 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.59 41.0 4.47e-01 72.5% 98.2%
5024287 103.5.1.11 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like › DUF2067 0.58 49.0 4.83e-01 95.7% 97.3%
3602038 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 50.0 2.87e-01 100.0% 24.7%
3425736 3525.1.1.1 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › BET 0.57 45.0 4.06e-01 85.5% 77.9%
5012947 1075.3.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC importer transmembrane domain fold › Type I ABC importer transmembrane domain fold › BPD_transp_1 0.57 41.0 2.91e-01 76.8% 80.0%
3560258 7579.1.1.81 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Arb2 0.56 48.0 3.19e-01 100.0% 79.1%
3903618 219.1.1.54 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C98 0.56 41.0 2.80e-01 82.6% 36.9%
3857891 148.1.3.19 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_3 0.55 40.0 3.74e-01 91.3% 60.0%
5043201 2004.11.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › PEP carboxykinase N-terminal domain › PEP carboxykinase N-terminal domain 0.54 45.0 3.33e-01 97.1% 87.4%
4949080 593.1.1.1 ↗ alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like › Cpn60_TCP1 0.53 42.0 2.73e-01 87.0% 63.1%
3355320 3525.1.1.1 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › BET 0.53 41.0 3.92e-01 85.5% 93.8%
3781191 2003.1.3.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain 0.52 44.0 3.15e-01 94.2% 97.1%
3271984 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.52 36.0 2.81e-01 72.5% 46.9%
3831178 3525.1.1.1 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › BET 0.52 41.0 3.90e-01 85.5% 93.8%
3232719 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.52 42.0 2.95e-01 95.7% 95.0%
5017776 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.51 39.0 2.77e-01 85.5% 93.3%
3487186 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.51 43.0 2.94e-01 98.6% 92.6%
3760279 2003.1.6.7 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Tubulin, Misat_Tub_SegII 0.50 44.0 3.03e-01 98.6% 30.6%
3444972 3525.1.1.1 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › BET 0.50 39.0 3.57e-01 84.1% 78.9%
D5 medium residues 585-644
PDB
D6 medium residues 704-793
PDB
D7 medium residues 795-860
PDB