Table 2.
Distribution of detected motifs in coding sequences and estimation of the percentage of the associated methylation.
| 5′-GGCC-3′ | 5′-GATC-3,′ | 5′-AGATCC-3′ | 5′-GGATCC-3′ | |||||
|---|---|---|---|---|---|---|---|---|
| Norm. I | Norm. II | Norm. I | Norm. II | Norm. I | Norm. II | Norm. I | Norm. II | |
| arCOG | ||||||||
| METABOLISM | ||||||||
| C: Energy production | 18.2 | 90.6 | 47.6 | 29.5 | 35 | 22.1 | 12.6 | 53.8 |
| E: Amino acid metabolism and transport | 12.4 | 98.1 | 59.5 | 41.3 | 43.8 | 30.6 | 15.7 | 78.3 |
| F: Nucleotide metabolism and transport | 1.8 | 100 | 45.5 | 40 | 36.4 | 34.8 | 9.1 | 57.1 |
| G: Carbohydrate metabolism and transport | 23.5 | 88.2 | 49 | 34.2 | 35.3 | 27.6 | 13.7 | 55.6 |
| H: Coenzyme metabolism and transport | 7.7 | 94.4 | 37.4 | 30.9 | 30.8 | 20.3 | 6.6 | 70 |
| I: Lipid metabolism and transport | 30.9 | 94.2 | 51.5 | 36.1 | 33.8 | 28.6 | 17.6 | 50 |
| P: Inorganic ion metabolism and transport | 10.9 | 80 | 41.3 | 25.9 | 34.8 | 20.5 | 6.5 | 50 |
| Q: Secondary metabolites biosynthesis, transport and catabolism | 13.8 | 87.5 | 48.3 | 30.6 | 37.9 | 14.3 | 10.3 | 87.5 |
| INFORMATION STORAGE AND PROCESSING | ||||||||
| J: Translation | 17.3 | 100 | 33.9 | 43.5 | 28.6 | 39.1 | 5.4 | 19 |
| K: Transcription | 7 | 96.9 | 22.5 | 37.8 | 19.4 | 30.6 | 3.1 | 9 |
| L: Replication, recombination and repair | 16.7 | 100 | 39.7 | 36.7 | 29.5 | 24.2 | 10.3 | 70.8 |
| CELLULAR PROCESSES AND SIGNALING | ||||||||
| D: Cell cycle control | 20 | 100 | 40 | 30 | 40 | 30 | 0 | 0 |
| M: Cell wall, membrane and envelope biogenesis | 8.3 | 90 | 47.9 | 30.6 | 31.3 | 17.5 | 16.7 | 54.5 |
| N: Cell motility | 0 | 0 | 50 | 25 | 25 | 0 | 25 | 50 |
| O: Post-translational modification, protein turnover, chaperones | 14.3 | 100 | 44.4 | 46.2 | 36.5 | 35 | 7.9 | 83.3 |
| T: Signal transduction mechanisms | 8.3 | 100 | 25 | 50 | 16.7 | 50 | 8.3 | 50 |
| U: Intracellular trafficking and secretion | 0 | 0 | 25 | 41.7 | 25 | 41.7 | 0 | 0 |
| V: Defense mechanisms | 7.8 | 100 | 20.8 | 19 | 18.2 | 13.9 | 2.6 | 50 |
| X: Mobilome | 6.1 | 100 | 21.2 | 14.3 | 15.2 | 0 | 6.1 | 50 |
| POORLY CHARACTERIZED | ||||||||
| R: General functional prediction only | 7.8 | 91.7 | 44.2 | 26.5 | 34.1 | 17.1 | 10.1 | 62.5 |
| S: Function unknown | 10.7 | 98.8 | 28.1 | 28.2 | 23.3 | 20.3 | 4.8 | 59.7 |
| Genes encoding tRNA | 81.6 | 100 | 8.2 | 12.5 | 8.2 | 12.5 | 0 | 0 |
| Genes encoding rRNA | 100 | 100 | 50 | 10 | 50 | 10 | 0 | 0 |
The percentage of genes containing the recognition sequence, 5′-GGCC-3′, 5′-AGATCC-3′, 5′-GGATCC-3,′ and/or the core motif 5′-GATC-3′ determined in Table 1, was calculated by counting the number of the corresponding motif in each genes. Then, this number was normalized using the total number of genes present either in each arCOG or in genes encoding tRNA or rRNA (Norm. I). To go further, the percentage of methylated motif was estimated by sorting methylated motif and normalizing by the total number of motif detected (Norm. II).