Table 2 Data collection
From: Secondary structural entropy in RNA switch (Riboswitch) identification
ID | Riboswitch | Organism (P/N) | Alteration | Grouping | References |
|---|---|---|---|---|---|
ID01 | Alpha Operon | Escherichia coli (N) | Slow-fast | Train | |
ID02 | ATP | Bacillus subtilis (P) | Enzyme | Test | [92] |
| Â | ATP[1] | Salmonella (N) | Enzyme | None | [73] |
ID03 | c-di-GMP | Geobacter sulfurreducens (N) | Ligand | Train | [40] |
ID04 | c-di-GMP | Candidatus Desulforudis (P) | Ligand | Test | [93] |
ID05 | Cobalamin | Escherichia coli (N) | Ligand | Train | [27] |
ID06 | Cobalamin | Bradyrhizobium japonicum (N) | Ligand | Train | [94] |
ID07 | Cobalamin | Salmonella (N) | Ligand | Test | [95] |
| Â | D. peptide[2] | Synechococcus sp. CC9902 (N) | Motif | None | [96] |
ID08 | Fluoride | Pseudomonas syringae (N) | Ligand | Train | [97] |
ID09 | Fluoride | Thermotoga petrophila (N) | Ligand | Train | [98] |
ID10 | Fluoride | Bacillus cereus (P) | Ligand | Test | [97] |
ID11 | FMN | Fusobacterium nucleatum (N) | Ligand | Train | |
ID12 | FMN | Escherichia coli (N) | Ligand | Train | |
ID13 | FMN | Bacillus subtilis (P) | Ligand | Test | |
| Â | glmS | T. tengcongensis (N) | None | None | |
| Â | glnA | Synechococcus elongatus (N) | Motif | None | [96] |
ID14 | Glycine | Fusobacterium nucleatum (N) | Ligand | Train | |
ID15 | Glycine | Bacillus subtilis (P) | Ligand | Test | [104] |
| Â | Hammerhead I | Schistosoma Mansoni (-) | None | None | |
| Â | Hammerhead II | Marine metagenome (-) | None | None | [108] |
ID16 | Lysine | Thermotoga maritima (N) | Ligand | Train | |
ID17 | Lysine | Bacillus subtilis (P) | Ligand | Test | [110] |
ID18 | Magnesium | Salmonella enterica (N) | Mg2+ | Train | |
ID19 | Magnesium | Escherichia coli (N) | Mg2+ | Train | [18] |
ID20 | Magnesium | Bacillus subtilis (P) | Mg2+ | Test | [19] |
ID21 | Moco | Escherichia coli (N) | Ligand | Train | [111] |
ID22 | pH-responsive | Escherichia coli (N) | pH | Train | [17] |
ID23 | pH-responsive | Serratia marcescens (N) | pH | Test | [17] |
ID24 | preQ1 II | Streptococcus pneumoniae (P) | Ligand | Train | |
ID25 | preQ1 I | Bacillus subtilis (P) | Ligand | Test | [113] |
ID26 | Purine (Adenine) | Vibrio vulnificus (N) | Ligand | Train | [39] |
ID27 | Purine (Adenine) | Bacillus subtilis (P) | Ligand | Test | [39] |
ID28 | Purine (Guanine) | Bacillus subtilis (P) | Ligand | Test | |
ID29 | ROSE-1 | Bradyrhizobium japonicum (N) | Heat | Train | |
ID30 | ROSE-2 | Escherichia coli (N) | Heat | Train | [21] |
ID31 | ROSE-2387 | Mesorhizobium loti (N) | Heat | Test | [21] |
ID32 | ROSE-N1 | Rhizobium (N) | Heat | Test | [21] |
ID33 | ROSE-P2 | Bradyrhizobium (N) | Heat | Train | [21] |
ID34 | SAH | Ralstonia solanacearum (N) | Ligand | Train | |
ID35 | SAM-I | T. tengcongensis (N) | Ligand | Train | [31] |
ID36 | SAM-I | Bacillus subtilis (P) | Ligand | Test | |
ID37 | SAM-II | Agrobacterium tumefaciens (N) | Ligand | Train | [120] |
ID38 | SAM-III (SMK) | Streptococcus gordonii (P) | Ligand | Train | [121] |
ID39 | SAM-III (SMK) | Enterococcus faecalis (P) | Ligand | Test | |
ID40 | SAM-IV | Streptomyces coelicolor (P) | Ligand | Train | [42] |
ID41 | SAM-IV | Mycobacterium tuberculosis (P) | Ligand | Test | [42] |
ID42 | SAM-SAH | Roseobacter (N) | Ligand | Train | [41] |
ID43 | SAM-SAH | Oceanibulbus indolifex (N) | Ligand | Test | [41] |
ID44 | SAM-V | Cand. P. ubique (N) | Ligand | Train | [124] |
ID45 | SAM-V | Cand. P. ubique (N) | Ligand | Test | [125] |
ID46 | THF | Eubacterium siraeum (P) | Ligand | Train | |
ID47 | THF | Clostridium kluyveri (P) | Ligand | Test | [126] |
ID48 | TPP | Escherichia coli (N) | Ligand | Train | |
ID49 | TPP | Bacillus subtilis (P) | Ligand | Test | |
ID50 | Tryptophan | Escherichia coli (N) | Complex | Train | |
ID51 | Tryptophan | Bacillus subtilis (P) | Complex | Test | |
ID52 | Tuco | Geobacter metallireducens (N) | Ligand | Test | [111] |
| Â | yxkD | Bacillus subtilis (P) | Motif | None | [76] |