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NC_053511.1__YP_010013457.1__J4U00_gp109__00109

Bact-Vir

NC_053511.1__YP_010013457.1__J4U00_gp109__00109

Identity

Accession:
NC_053511 ↗
Kingdom:
phage

Quality

74.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vilmaviridae› Bromdenvirus› Mycobacterium_phage_DyoEdafos

TaxID: 2599860

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 11-68
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3onqA03 1.10.10.2840 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › PucR C-terminal helix-turn-helix domain 0.69 58.0 4.54e-01 98.3% 52.7%
3qqaA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.69 50.0 5.04e-01 79.3% 94.9%
2i2xB01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.65 44.0 3.77e-01 70.7% 67.0%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.65 45.0 3.75e-01 74.1% 47.2%
2qbyB03 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 0.64 55.0 4.81e-01 100.0% 100.0%
2kvcA01 1.10.150.430 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF3349, helical bundle 0.63 53.0 4.61e-01 93.1% 65.9%
2looA02 1.10.10.1740 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Transmembrane protein 14-like 0.61 43.0 4.04e-01 75.9% 93.3%
5a48B00 3.30.420.610 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › LOTUS domain-like 0.59 50.0 4.29e-01 98.3% 77.1%
1js8A01 1.10.1280.10 Mainly Alpha › Orthogonal Bundle › di-copper center containing domain from catechol oxidase › Di-copper center containing domain from catechol oxidase 0.57 45.0 2.93e-01 87.9% 51.4%
6j3eA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 41.0 3.07e-01 77.6% 31.6%
3llkA02 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.55 46.0 3.57e-01 98.3% 90.2%
6rxaA01 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.55 43.0 3.83e-01 87.9% 78.2%
4o6kA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 46.0 3.57e-01 98.3% 70.6%
4by6D02 1.25.40.800 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 37.0 2.59e-01 72.4% 26.7%
2fgeA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.54 43.0 3.01e-01 100.0% 81.2%
5bukB00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 45.0 2.75e-01 100.0% 42.3%
3rotA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 44.0 3.50e-01 98.3% 59.9%
3ckdA02 1.20.58.360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Shigella T3SS effector IpaH defines 0.53 38.0 3.03e-01 100.0% 36.3%
2qnlA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.51 42.0 3.21e-01 100.0% 65.4%
1zq3P00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.51 39.0 3.71e-01 96.6% 70.6%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4373546 604.39.1.5 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › ECF_trnsprt 0.65 52.0 3.71e-01 89.7% 73.5%
4101595 140.1.1.0 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.62 43.0 2.85e-01 77.6% 18.7%
3741114 223.2.1.29 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › DENND11 0.59 48.0 3.48e-01 89.7% 35.0%
3475373 1128.1.1.2 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR_2 0.55 38.0 3.58e-01 100.0% 57.3%
415175 109.19.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Immunity Factor for SPN › Immunity Factor for SPN › IFS 0.54 36.0 2.69e-01 70.7% 39.9%
3589151 829.1.1.2 ↗ a+b duplicates or obligate multimers › NinB › NinB › NinB › HNHc_6 0.53 38.0 2.96e-01 100.0% 36.0%
5083165 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 41.0 2.86e-01 96.6% 77.3%
4446824 2003.1.2.14 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO,FAO_M 0.52 41.0 2.50e-01 89.7% 45.1%
4947979 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 44.0 4.17e-01 100.0% 90.0%