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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 [90,91]
ID02 ATP Bacillus subtilis (P) Enzyme Test [92]
  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]
  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 [99,100]
ID12 FMN Escherichia coli (N) Ligand Train [20,101]
ID13 FMN Bacillus subtilis (P) Ligand Test [99-101]
  glmS T. tengcongensis (N) None None [75,76,102,103]
  glnA Synechococcus elongatus (N) Motif None [96]
ID14 Glycine Fusobacterium nucleatum (N) Ligand Train [104-106]
ID15 Glycine Bacillus subtilis (P) Ligand Test [104]
  Hammerhead I Schistosoma Mansoni (-) None None [34,107]
  Hammerhead II Marine metagenome (-) None None [108]
ID16 Lysine Thermotoga maritima (N) Ligand Train [109,110]
ID17 Lysine Bacillus subtilis (P) Ligand Test [110]
ID18 Magnesium Salmonella enterica (N) Mg2+ Train [18,20]
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 [40,112]
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 [39,114]
ID29 ROSE-1 Bradyrhizobium japonicum (N) Heat Train [21,22]
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 [40,115]
ID35 SAM-I T. tengcongensis (N) Ligand Train [31]
ID36 SAM-I Bacillus subtilis (P) Ligand Test [116-119]
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 [121-123]
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 [126,127]
ID47 THF Clostridium kluyveri (P) Ligand Test [126]
ID48 TPP Escherichia coli (N) Ligand Train [30,128-130]
ID49 TPP Bacillus subtilis (P) Ligand Test [26,129]
ID50 Tryptophan Escherichia coli (N) Complex Train [8,131]
ID51 Tryptophan Bacillus subtilis (P) Complex Test [132,133]
ID52 Tuco Geobacter metallireducens (N) Ligand Test [111]
  yxkD Bacillus subtilis (P) Motif None [76]
  1. Collected sequences from literature observed to have more than one secondary structure. P corresponds to gram-positive and N corresponds to gram-negative. Genomic locations are available in Table 3.
  2. [1]Table 2: This sequence overlaps codons. pH also has a role in alteration of structure.
  3. [2]Table 2: Downstream-peptide.