Table 3. Functional categories in environmental and clinical P. putida isolates.
| Functional categories | KT2440 | BIRD-1 | DOT-T1E | F1 | GB-1 | W619 | S16 | HB13667 | H8234 | HB4184 | HB3267 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors, Vitamins, Prosthetic Groups, Pigments | 387 (9.6) | 314 (8.4) | 321 (7.9) | 380 (10) | 361 (10) | 374 (9.9) | 311 (8.2) | 331 (9.5) | 343 (8) | 304 (7.9) | 307 (7.9) |
| Cell Wall and Capsule | 183 (4.5) | 191 (5.1) | 196 (4.9) | 155 (4.1) | 137 (3.8) | 168 (4.5) | 176 (4.6) | 174 (5) | 196 (4.6) | 176 (4.6) | 177 (4.6) |
| Resistance to biocides | 124 (3.1) | 88 (2.4) | 111 (2.8) | 86 (2.3) | 29 (0.8) | 94 (2.5) | 103 (2.7) | 154 (4.41) | 152 (3.6) | 132 (3.4) | 137 (3.5) |
| *Heavy metal homeostasis and resistance | 81 (2) | 46 (1.2) | 59 (1.5) | 64 (1.6) | 14 (0.4) | 69 (1.8) | 65 (1.7) | 112 (3.2) | 110 (2.6) | 94 (2.5) | 89 (2.3) |
| Potassium metabolism | 49 (1.2) | 38 (1) | 31 (0.8) | 21 (0.6) | 2 (0.1) | 21 (0.6) | 31 (0.8) | 34 (1) | 34 (0.8) | 28 (0.7) | 32 (0.8) |
| Miscellaneous | 85 (2.1) | 56 (1.5) | 65 (1.6) | 90 (2.4) | 91 (2.5) | 85 (2.3) | 52 (1.3) | 55 (1.6) | 75 (1.8) | 55 (1.4) | 49 (1.3) |
| Phages, Prophages, Transposable elements, Plasmids | 3 (0.07) | 5 (0.13) | 11 (0.27) | 1 (0.03) | 0 (0) | 2 (0.05) | 16 (0.42) | 41 (1.18) | 40 (0,94) | 35 (0.91) | 31 (0.8) |
| Membrane Transport | 202 (5) | 158 (4.2) | 225 (5.6) | 145 (3.8) | 145 (4.0) | 167 (4.4) | 162 (4.3) | 196 (5.6) | 236 (5.5) | 209 (5.5) | 183 (4.7) |
| *Protein secretion system, Type II | 10 (0.25) | 10 (0.27) | 10 (0,25) | 10 (0.26) | 10 (0.28) | 36 (0.95) | 10 (026) | 19 (0.54) | 17 (0.4) | 10 (0,26) | 21 (0,54) |
| *Protein and nucleoprotein secretion system, Type IV | 18 (0.45) | 19 (0.51) | 28 (0.69) | 18 (0.47) | 19 (0.52) | 19 (0.51) | 18 (0.48) | 27 (0.78) | 54 (1.23) | 28 (0,73) | 27 (0.70) |
| *Secretion system type I-Fimbriae | 5 (0.12) | 5 (0.13) | 5 (0.12) | 5 (0.13) | 5 (0.13) | 5 (0.13) | 5 (0.13) | 7 (0.20) | 5 (0.12) | 5 (0.13) | 7 (0.18) |
| Iron acquisition and metabolism | 107 (2.7) | 66 (1.8) | 60 (1.5) | 115 (3.0) | 82 (2.3) | 110 (2.9) | 54 (1.4) | 57 (1.6) | 70 (1.6) | 61 (1.6) | 56 (1.4) |
| RNA Metabolism | 251 (6.2) | 132 (3.5) | 138 (3.4) | 209 (5.5) | 206 (5.7) | 213 (5.7) | 154 (4.1) | 152 (4.4) | 140 (3.3) | 148 (3.9) | 149 (3.9) |
| Nucleosides and Nucleotides | 131 (3.3) | 125 (3.3) | 138 (3.4) | 126 (3.4) | 132 (3.6) | 138 (3.7) | 126 (3.3) | 129 (3.7) | 136 (3.2) | 131 (3.4) | 127 (3.3) |
| Protein Metabolism | 258 (6.4) | 273 (7.3) | 267 (6.6) | 251 (6.6) | 245 (6.8) | 246 (6.6) | 266 (7.0) | 242 (6.9) | 264 (6.2) | 249 (6.5) | 264 (6.8) |
| Cell Division and Cell Cycle | 33 (0.81) | 37 (1.00) | 35 (0.87) | 32 (0.84) | 34 (0.94) | 33 (0.88) | 33 (0.87) | 36 (1.03) | 28 (0.66) | 36 (0.94) | 36 (0.93) |
| Motility and Chemotaxis | 77 (1.9) | 118 (3.2) | 130 (3.2) | 82 (2.2) | 80 (2.2) | 78 (2.1) | 117 (3.1) | 120 (3.4) | 120 (2.8) | 122 (3.2) | 117 (3.0) |
| Regulation and Cell signaling | 100 (2.5) | 113 (3.0) | 109 (2.7) | 111 (2.9) | 112 (3.1) | 109 (2.9) | 116 (3.1) | 118 (3.4) | 122 (2.9) | 111 (2.9) | 110 (2.8) |
| Secondary Metabolism | 5 (0.12) | 5 (0.13) | 7 (0.17) | 14 (0.37) | 5 (0.13) | 14 (0.37) | 5 (0.13) | 5 (0.14) | 5 (0.12) | 5 (0.13) | 5 (0.13) |
| DNA Metabolism | 139 (3.4) | 125 (3.3) | 140 (3.5) | 133 (3.5) | 127 (3.5) | 130 (3.5) | 140 (3.7) | 154 (4.4) | 140 (3.3) | 151 (3.9) | 143 (3.8) |
| Fatty Acids, Lipids, and Isoprenoids | 136 (3.4) | 178 (4.8) | 188 (4.7) | 147 (3.9) | 128 (3.5) | 140 (3.7) | 169 (4.5) | 195 (5–6) | 200 (4.7) | 185 (4.8) | 185 (4.8) |
| * Phospholipids | 35 (0.87) | 44 (1.12) | 45 (1.12) | 37 (0.97) | 38 (1.08) | 34 (0.95) | 47 (1.24) | 48 (1.38) | 54 (1.28) | 47 (1.24) | 48 (1.24) |
| Nitrogen Metabolism | 16 (0.40) | 35 (0.94) | 39 (0.97) | 34 (0.89) | 23 (0.64) | 25 (0.67) | 33 (0.87) | 31 (0.89) | 36 (0.84) | 33 (0.86) | 33 (0.85) |
| Dormancy and Sporulation | 5 (0.12) | 3 (0.08) | 4 (0.10) | 5 (0.13) | 4 (0.11) | 5 (0.13) | 3 (0.08) | 3 (0.09) | 4 (0.09) | 3 (0.08) | 3 (0.08) |
| Respiration | 183 (4.5) | 145 (3.9) | 151 (3.8) | 167 (4.4) | 175 (4.8) | 171 (4.6) | 164 (4.3) | 154 (4.4) | 159 (3.7) | 138 (3.6) | 161 (4.1) |
| Stress Response | 190 (4.7) | 180 (4.8) | 186 (4.6) | 170 (4.7) | 170 (4.7) | 181 (4.8) | 184 (4.9) | 198 (5.7) | 204 (5.0) | 195 (5.1) | 194 (5.0) |
| *Oxidative stress | 95 (2.4) | 85 (2.3) | 87 (2.2) | 64 (1.7) | 58 (1.6) | 76 (2.0) | 80 (2.1) | 95 (2.7) | 91 (2.1) | 88 (2.3) | 89 (2.3) |
| *Osmotic stress | 22 (0,54) | 36 (0.96) | 37 (0.92) | 22 (0.58) | 33 (0,91) | 26 (0.69) | 32 (0.84) | 37 (1.06) | 46 (1.08) | 40 (1.04) | 40 (1.04) |
| **Choline and Betaine Uptake and Betaine Biosynthesis | 18 (0.47) | 26 (0.70) | 30 (0,74) | 17 (0,45) | 27 (0.74) | 20 (0,53) | 25 (0.66) | 30 (0.86) | 38 (0.89) | 33 (0.86) | 33 (0.85) |
| Metabolism of Aromatic Compounds | 133 (3.3) | 136 (3.6) | 187 (4.6) | 168 (4.4) | 152 (4.2) | 153 (4.1) | 100 (2.6) | 123 (3.5) | 152 (3.6) | 119 (3.1) | 118 (3.1) |
| Amino Acids and Derivatives | 614 (15.2) | 616 (16.5) | 646 (16.0) | 563 (14.8) | 555 (15.2) | 571 (15.2) | 629 (16.6) | 636 (18.2) | 689 (16.1) | 635 (16.7) | 647 (16.7) |
| *Cysteine Biosynthesis | 18 (0.45) | 26 (0.70) | 26 (0.65) | 20 (0.53) | 21 (0.58) | 20 (0.53) | 26 (0.69) | 28 (0.80) | 27 (0.63) | 28 (0.73) | 27 (0.7) |
| *Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 27 (0.67) | 35 (0.93) | 41 (1.01) | 28 (0.73) | 34 (0.94) | 29 (0.77) | 41 (1.08) | 42 (1.20) | 43 (1.01) | 41 (1.07) | 44 (1.13) |
| *Histidine Degradation | 7 (0.17) | 8 (0,21) | 8 (0.20) | 8 (0.21) | 8 (0.22) | 8 (0.21) | 8 (0.21) | 9 (0.26) | 8 (0.19) | 9 (0.23) | 9 (0.23) |
| Sulfur Metabolism | 79 (2.0) | 67 (1.8) | 83 (2.1) | 81 (2.1) | 122 (3.4) | 69 (1.8) | 82 (2.2) | 91 (2.6) | 127 (3.0) | 89 (2.3) | 93 (2.4) |
| *Organic sulfur assimilation | 45 (1.1) | 29 (0.78) | 44 (1.09) | 43 (1.13) | 83 (2.3) | 30 (0.80) | 43 (1.13) | 51 (1.46) | 86 (2.02) | 54 (1.41) | 54 (1–40) |
| Phosphorus Metabolism | 59 (1.5) | 48 (1.29) | 49 (1.22) | 55 (1.44) | 59 (1.63) | 48 (1.28) | 49 (1.29) | 55 (1.58) | 52 (1.22) | 50 (1.30) | 49 (1.27) |
| Carbohydrates | 457 (11.3) | 445 (11.9) | 471 (11.7) | 443 (11.6) | 417 (11.5) | 387 (10.3) | 464 (12.2) | 444 (12.7) | 509 (11.9) | 438 (11.4) | 440 (11.4) |
| Total genes with functional category | 4029 | 3732 | 4028 | 3808 | 3618 | 3755 | 3788 | 3489 | 4261 | 3833 | 3864 |
Numbers indicate the number of genes involved in a given functional category. In parentheses, percentages considering the total of genes with functional category.