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Table 3 Two-level functional classification of identified RNA motif-regulated genes

From: Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

Overall functional categories (OFC)

Specific functional categories (SFC)

1. Coenzyme metabolism

B12 biosynthesis; Thiamin biosynthesis; Riboflavin biosynthesis; Queuosine biosynthesis; Folate biosynthesis; Molybdenum cofactor biosynthesis

2. Coenzyme uptake

B12 & precursor transporters; Thiamin & precursor transporters; Riboflavin transporters; Queuosine & precursor transporters; Folate transporters

3. Amino acid metabolism

Methionine biosynthesis; Methionine & SAM recycling; Cysteine biosynthesis; Lysine biosynthesis; Glycine metabolism; Serine metabolism; Ornithine degradation; Leucine biosynthesis; Histidine biosynthesis; Threonine biosynthesis; Tryptophan biosynthesis; Amino acid biosynthesis

4. Amino acid uptake

Methionine transporters; Lysine transporters; Glycine transporters; Histidine transporters; Amino acid transporters

5. Secondary metabolism

Aminosugar biosynthesis; Citric acid cycle; Urea and agmatine utilization

6. Metal homeostasis

Cobalt transporters; Molybdenum & tungsten transporters; Magnesium transporters; Potassium transporters

7. Nucleobase metabolism

Purine metabolism; Pyrimidine metabolism

8. Nucleobase uptake

Purine & precursor transporters; Pyrimidine transporters

9. Protein synthesis

Ribosome biogenesis; Amino acyl-tRNA synthetases

10. Miscellaneous

Isozymes of B12-dependent enzymes; Multidrug resistance transporter; Polysaccharide degradation; Other or unknown functional roles