| Pathway ID | CON–CON | CON–Ba | MO–CON | MO–Ba |
| Metabolic pathways | 4,682,208 | 4,174,213 | 4,745,730 | 4,361,700 | Biosynthesis of secondary metabolites | 2,209,745 | 1,810,849 | 2,179,152 | 1,915,360 | Microbial metabolism in diverse environments | 1,307,783 | 1,086,358 | 1,406,392 | 1,153,645 | Biosynthesis of amino acids | 935,922 | 726,328 | 837,171 | 752,132 | Carbon metabolism | 690,094 | 626,715 | 748,673 | 676,111 | ABC transporters | 562,045 | 510,720 | 557,498 | 498,189 | Ribosome | 509,757 | 492,115 | 488,196 | 502,658 | Two-component system | 494,295 | 477,370 | 456,205 | 459,384 | Purine metabolism | 411,870 | 411,283 | 417,627 | 423,338 | Quorum sensing | 343,410 | 312,450 | 349,552 | 311,760 | Glycolysis/gluconeogenesis | 315,325 | 296,563 | 318,816 | 308,709 | Pyrimidine metabolism | 297,474 | 328,256 | 282,218 | 328,621 | Pyruvate metabolism | 298,578 | 270,273 | 313,132 | 280,704 | Amino sugar and nucleotide sugar metabolism | 308,034 | 288,582 | 262,744 | 284,024 | Porphyrin and chlorophyl metabolism | 263,796 | 262,966 | 249,901 | 251,081 | Aminoacyl–tRNA biosynthesis | 248,535 | 255,589 | 249,565 | 258,440 | Carbon fixation pathways in prokaryotes | 225,694 | 243,065 | 268,152 | 265,767 | Cysteine and methionine metabolism | 247,849 | 249,550 | 235,448 | 246,057 | Starch and sucrose metabolism | 286,184 | 240,486 | 211,589 | 232,266 | Alanine, aspartate, and glutamate metabolism | 224,484 | 215,751 | 224,673 | 226,689 |
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