TABLE 1.
fModule annotation and explained variancea
| fModule | Description | # of genes | Explained variance | fModule | Description | # of genes | Explained variance |
|---|---|---|---|---|---|---|---|
| 1 | Fatty Acid Metabolism | 3 | 0.21% | 43 | Phenylalanine Catabolism | 11 | 0.18% |
| 2 | Nitrogen metabolism | 6 | 2.63% | 44 | Beta-alanine catabolism | 10 | 0.31% |
| 3 | RidA | 1 | 0.98% | 45 | Spermidine and propandiamine catabolism | 17 | 0.27% |
| 4 | Transcriptional regulation | 13 | 0.32% | 46 | Butyrolactam catabolism | 5 | 0.15% |
| 5 | Benzoate catabolism | 13 | 0.23% | 47 | Transcriptional regulation and cell:surface adhesion | 6 | 0.65% |
| 6 | Glycine, serine, and threonine metabolism | 9 | 0.14% | 48 | Acetic acid stress | 7 | 0.57% |
| 7 | Choline, betaine, and carnitine catabolism | 22 | 0.22% | 49 | 4-Hydroxyvalerate catabolism | 2 | 0.45% |
| 8 | Propanediamine catabolism | 22 | 0.61% | 50 | 1,4-Butanediol catabolism | 7 | 0.34% |
| 9 | Maintenance of lipid asymmetry (Mla) system | 14 | 0.50% | 51 | Phenolic acid stress | 19 | 0.24% |
| 10 | Bioreactor growth | 3 | 0.40% | 52 | Flagellar biosynthesis | 25 | 0.39% |
| 11 | Levulinic acid catabolism | 16 | 0.52% | 53 | Fatty acid metabolism | 11 | 0.88% |
| 12 | Biotin biosynthesis and pyruvate carboxylase | 9 | 1.24% | 54 | ParB | 1 | 0.29% |
| 13 | Molybdopterin biosynthesis and benzaldehyde tolerance | 20 | 0.42% | 55 | Lactic acid stress | 14 | 0.78% |
| 14 | 4-Coumarate and ferulate catabolism | 5 | 0.15% | 56 | Thymine degradation | 6 | 0.20% |
| 15 | Glutamate metabolism | 3 | 1.09% | 57 | Branched-chain Amino acid biosynthesis | 5 | 7.48% |
| 16 | Benzoate, 4-coumarate, and ferulate catabolism | 16 | 1.96% | 58 | Fatty acid catabolism | 4 | 0.64% |
| 17 | Pyrroloquinoline biosynthesis and short-chain alcohol catabolism | 20 | 0.41% | 59 | Thiamine diphosphate biosynthesis | 6 | 2.45% |
| 18 | Phenylacetate catabolism | 16 | 0.30% | 60 | 4-Aminobutyric acid catabolism | 7 | 0.18% |
| 19 | Phosphoenolpyruvate:sugar phosphotransferase system | 2 | 0.37% | 61 | Nitrogen metabolism | 6 | 0.20% |
| 20 | 4-Coumarate, ferulate, and catabolic intermediate stress tolerance | 6 | 0.34% | 62 | Galacturonic acid and glucuronic acid catabolism | 11 | 0.26% |
| 21 | Arginine metabolism | 14 | 3.12% | 63 | Methionine biosynthesis | 5 | 3.80% |
| 22 | Cobalamin biosynthesis and ethanolamine catabolism | 22 | 0.50% | 64 | NadC | 1 | 2.51% |
| 23 | Uncharacterized | 4 | 0.71% | 65 | Glutamate transport | 12 | 0.36% |
| 24 | Nitrogen stress sensor and glycogen biosynthesis | 3 | 0.43% | 66 | Proline metabolism | 2 | 2.05% |
| 25 | Bioreactor growth | 14 | 0.68% | 67 | Valine biosynthesis | 3 | 3.71% |
| 26 | Uncharacterized | 11 | 0.27% | 68 | Lysine metabolism | 18 | 0.60% |
| 27 | Membrane to surface adhesion | 5 | 0.96% | 69 | Histidine biosynthesis | 2 | 3.82% |
| 28 | Ferulate and catabolic intermediate catabolism | 9 | 0.32% | 70 | Butyrate catabolism | 9 | 0.34% |
| 29 | Transport of butylamine-containing compounds | 6 | 0.16% | 71 | HisA | 1 | 0.50% |
| 30 | Histidine biosynthesis | 11 | 6.89% | 72 | Lysine metabolism | 5 | 0.27% |
| 31 | Protocatechuate stress | 8 | 0.58% | 73 | L-Lysine catabolism | 3 | 0.24% |
| 32 | Nitrogen assimilation | 4 | 0.95% | 74 | Tryptophan biosynthesis | 9 | 8.47% |
| 33 | Biotin biosynthesis and isopentanol/isoprenol catabolism | 12 | 0.35% | 75 | Uncharacterized | 6 | 1.86% |
| 34 | Improved fitness factors | 7 | 1.91% | 76 | Sodium tolerance | 21 | 0.58% |
| 35 | Uncharacterized | 6 | 1.12% | 77 | Fatty acid metabolism | 2 | 0.15% |
| 36 | Possible Tween-20 catabolism | 12 | 0.24% | 78 | Possible butyrate metabolism | 7 | 0.18% |
| 37 | Lipopolysaccharide biosynthesis | 12 | 0.27% | 79 | Fatty ester metabolism | 7 | 0.32% |
| 38 | RuvC | 1 | 0.37% | 80 | No gene | 0 | 0.21% |
| 39 | PP_1410 | 1 | 0.18% | 81 | SerA | 1 | 1.32% |
| 40 | Acetate catabolism | 3 | 0.23% | 82 | ProI | 1 | 0.44% |
| 41 | Hexanoate and valerate catabolism | 10 | 0.20% | 83 | Beta-ketoadipate and levulinic acid stress | 4 | 0.22% |
| 42 | NADH:ubiquinone oxidoreductase I | 14 | 1.68% | 84 | Nitrate metabolism | 3 | 0.15% |
a
Functional annotations for each fModule, the number of genes in each fModule, and the proportion of the RB-TnSeq data set variance explained by each fModule. 543 unique genes are contained within the 84 fModules. Full details for each fModule are available at https://fmodules.github.io/putida.