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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00556

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00556

Identity

Kingdom:
phage

Quality

74.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 7-63
PDB
Domain cluster: representative
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 48.0 4.52e-01 71.9% 59.4%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 45.0 3.51e-01 71.9% 31.5%
2wpvE00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 54.0 3.49e-01 91.2% 33.6%
3etuA01 1.10.287.3290 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 45.0 4.34e-01 77.2% 67.7%
8h6rA01 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.61 55.0 4.77e-01 100.0% 96.5%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.60 52.0 4.87e-01 98.2% 87.1%
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.59 52.0 4.39e-01 100.0% 71.0%
2w82A03 1.10.10.1190 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Antirestriction protein ArdA, domain 3 0.58 37.0 3.66e-01 87.7% 59.7%
2kwhA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 37.0 3.81e-01 77.2% 71.4%
1sg7A00 1.10.1740.70 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › ChaB 0.55 39.0 3.58e-01 75.4% 73.3%
3gfaA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.55 45.0 3.25e-01 100.0% 71.9%
1b04A03 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.55 47.0 4.63e-01 98.2% 91.9%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.54 46.0 3.69e-01 100.0% 69.4%
4uwmA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.54 45.0 2.79e-01 94.7% 23.2%
4b09B02 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 0.54 46.0 3.91e-01 100.0% 78.6%
3hi0A02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.53 43.0 3.03e-01 91.2% 78.7%
1kgqA01 1.10.166.10 Mainly Alpha › Orthogonal Bundle › Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 › Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain 0.52 42.0 4.05e-01 96.5% 92.9%
1i94H01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.52 43.0 3.92e-01 94.7% 100.0%
1z6mA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 35.0 2.86e-01 93.0% 36.0%
1ug8A00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.51 42.0 3.67e-01 93.0% 79.3%
5mmjh01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.51 41.0 3.83e-01 93.0% 82.7%
2l3oA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.51 41.0 3.37e-01 100.0% 74.2%
3pw3D00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.50 41.0 2.55e-01 93.0% 45.9%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3248621 109.4.1.1463 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF28490 0.65 52.0 2.80e-01 91.2% 11.9%
3199316 5069.1.1.4 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Ferric_reduct 0.62 48.0 3.23e-01 87.7% 25.8%
4474140 320.2.1.1 ↗ a+b two layers › R3H domain-like › Ribosomal protein S8, N-terminal domain › Ribosomal protein S8, N-terminal domain › Ribosomal_S8 0.59 42.0 4.05e-01 96.5% 66.2%
4187493 603.1.1.103 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF29732 0.59 50.0 3.82e-01 100.0% 73.1%
3974001 7579.1.1.102 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S9, Hydrolase_4 0.56 45.0 2.92e-01 96.5% 41.3%
3520924 206.1.1.88 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › EcKL, DUF1679 0.55 42.0 2.37e-01 91.2% 17.9%
4599024 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.53 45.0 3.98e-01 96.5% 76.5%
4257661 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.53 45.0 3.97e-01 100.0% 96.7%
3763861 197.1.1.1 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › FERM_M 0.53 43.0 3.20e-01 94.7% 58.7%
4990916 283.2.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.52 45.0 3.71e-01 94.7% 81.0%
3562229 197.1.1.1 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › FERM_M 0.51 41.0 3.28e-01 96.5% 51.1%