Supplementary Table 1: List of modules and their associated KOs. Modules Description List of KOs K00656/K00132/K04072/K04073/K00001/K00121/K11440/ MF0001 ethanol production (formate pathway) K13953/K13954 MF0002 ethanol production (CO2 pathway) K00001/K00121/K04072/K11440/K13953/K13954 MF0003 acetylglucosamine degradation K00884/K01443/K02564/K02802/K02803/K02804 MF0004 putrescine degradation K00137/K09251/K09471/K09472 acetylneuraminate and acetylmannosamine MF0005 K01639/K00885/K01788 degradation MF0006 urea degradation K14048/K01941/K01457/K01428/K01429/K01430 MF0007 phenylalanine degradation K00832/K00812/K00813/K11358/K00817 tyrosine degradation (hydroxyphenylacetaldehyde MF0008 K00832/K00812/K00813/K11358/K00817/K00055 pathway) MF0009 tryptophan degradation K01667 MF0010 tyrosine degradation (phenol pathway) K01668 MF0011 aspartate degradation (oxaloacetate pathway) K00812/K00813/K11358 MF0012 aspartate degradation (fumarate pathway) K01744 MF0013 glutamate degradation (crotonyl-CoA pathway) K00260/K15371/K00261/K00262/K01615/K01039/K01040 glutamate degradation (4-aminobutanoate MF0014 K01580 pathway) MF0015 glutamate degradation (methylaspartate pathway) K01846/K04835 MF0016 glycine degradation K00281/K00605/K00382/K00282/K00283 MF0017 alanine degradation (racemase pathway) K01775/K00285 MF0018 proline degradation (glutamate pathway) K13821/K00318/K00294 MF0019 proline degradation (aminopentanoate pathway) K01777/K10793/K10794/K10795/K10796 K00826/K00248/K00249/K01692/K01782/K01825/K00020/ MF0020 valine degradation K00382/K11381/K00140/K00822/K07250 MF0021 leucine degradation K00826/K00249/K13766/K01640/K00382/K11381/K01968 K00826/K00248/K00249/K01692/K01782/K01825/K00626/ MF0022 isoleucine degradation K00632/K00382/K11381 MF0023 methionine degradation (cysteine pathway) K00789/K00558/K01251 MF0024 methionine degradation (mercaptan pathway) K01761 MF0025 alanine degradation (glutamate pathway) K00259 MF0026 cysteine biosynthesis/homocysteine degradation K01697/K01758 MF0027 cysteine degradation K01758/K01760 MF0028 serine degradation K01752/K01753 MF0029 threonine degradation (glycine pathway) K00060/K00639/K01620/K00132/K04072/K04073 MF0030 threonine degradation (formate pathway) K01754/K00656 MF0031 asparagine degradation K01424 MF0032 glutamine degradation (ammonia pathway) K01425 MF0033 cysteine degradation (mercaptopyruvate pathway) K00812/K01011/K00813/K11358 MF0034 glutamine degradation (oxoglutarate pathway) K00265/K00266 arginine degradation (agmatine deiminase MF0035 K01583/K01584/K01585/K02626/K10536/K12251 pathway) arginine degradation (ornithine decarboxylase MF0036 K01476/K01581 pathway) arginine degradation (AST/succinyltransferase MF0037 K00673/K01484/K00840/K06447/K05526 pathway) lysine fermentation to acetate and butyrate (3,6- MF0039 K01843/K01844/K00248 diaminohexanoate pathway) MF0040 lysine degradation (cadaverine pathway) K01582 MF0041 histidine degradation K01745/K01712/K01468/K01479/K01458/K00603/K13990 MF0042 4-aminobutyrate degradation K00823/K07250/K00135/K14534 MF0043 arginine degradation (agmatinase pathway) K01583/K01584/K01585/K02626/K01480 MF0044 glycocholate degradation K01442/K00076 MF0045 trehalose degradation K01226/K01194/K05342 MF0046 sucrose degradation K01193/K00847 K01220/K01819/K00917/K08302/K01635/K02786/K02787/ MF0047 lactose and galactose degradation (PTS) K02788 MF0048 lactose degradation K12111/K01190/K12308 MF0049 maltose degradation K00691/K01838 MF0050 melibiose degradation K07406/K07407 MF0051 sucrose degradation (Actinobacteria) K00690/K00847/K01792/K01835 chondroitin sulfate and dermatan sulfate MF0052 K08961 degradation MF0053 allose degradation K00881/K01808 MF0054 arabinose degradation K01804 MF0055 xylose degradation K01805/K00854 MF0056 galactose degradation (Leloir pathway) K01785/K00849/K00965/K01784/K01838 alpha-D-glucose and alpha-D-glucose 1-phosphate MF0057 K00117/K00845/K01053/K01085/K01792/K01835 degradation MF0058 fructose degradation K00882 MF0059 rhamnose degradation K01813/K00848/K01629/K01803 MF0060 ribose degradation K00852 MF0061 mannose degradation K01809 K01176/K07405/K01200/K01208/K00688/K00705/K01187/ MF0062 starch degradation K01178/K01182/K01214 MF0063 fructan degradation K03332 MF0064 pectin degradation K01051/K01184/K01213 pectin degradation - 5-dehydro-4-deoxy-D- MF0065 K01728/K01730/K01815/K00874/K01625 glucuronate degradation MF0066 glycogen metabolism K00975/K00703/K00700/K00688/K01187/K00705 MF0067 PHB production K00023 MF0068 glucarate degradation K01706/K13877/K00042/K01630/K11529 MF0069 galactarate degradation K01708/K13877/K00042/K01630/K11529 MF0070 galactonate degradation K01684/K00883/K01631 MF0071 D-galacturonate degradation K01812/K00041/K01685/K00874 MF0072 ribitol degradation K00875/K01783 MF0073 sorbitol degradation (dehydrogenase) K00008 MF0074 mannitol degradation K00009 sorbitol degradation (phosphotransferase)/sorbose MF0075 K00068 degradation MF0076 arabitol degradation K00854 MF0077 galactitol degradation K00094/K00917/K01635/K08302/K01803 MF0078 xylitol degradation K05351/K00854 MF0079 bifidobacterium shunt K00616/K00615/K01807/K01808/K01783/K01621 K00844/K00845/K01810/K06859/K00850/K01623/K01624/ MF0080 Glycolysis (preparatory phase) K01803 MF0081 Glycolysis (pay-off phase) K00134/K00927/K01834/K01689/K00873 MF0082 pentose phosphate pathway (oxidative branch) K00036/K01057/K07404/K00033 MF0083 pyruvate dehydrogenase complex K00163/K00382/K00627/K00161/K00162 MF0084 pyruvate:ferredoxin oxidoreductase K00169/K00170/K00171/K00172 MF0085 pyruvate:formate lyase K00656 K01647/K01681/K01682/K00031/K00030/K01676/K01679/ K00024/K00116/K00164/K00658/K00382/K01902/K01903/ MF0086 TCA cycle K00239/K00240/K00241/K00242/K00244/K00245/K00246/ K00247/K01677/K01678 K01647/K01681/K01682/K00031/K00030/K01637/K01638/ MF0087 TCA cycle (Mycobacterium pathway) K00024/K00239/K00240/K00241/K00242/K00244/K00245/ K00246/K00247 K01647/K01681/K01682/K00031/K00030/K01676/K01679/ MF0088 TCA cycle (Helicobacter pathway) K00116/K00174/K00175/K00176/K00177/K01028/K01677/ K01678 MF0089 Entner-Doudoroff pathway I K01690/K01625 MF0090 pentose phosphate pathway (non-oxidative branch) K01807/K01808/K01783/K00615/K00616 MF0091 beta-D-glucuronide and D-glucuronate degradation K00040/K00874/K01195/K01686/K01812 K00677/K02535/K02536/K03269/K00748/K00912/K02527/ MF0092 kdo2-lipid A synthesis K02517/K02560 K01938/K01491/K00297/K15023/K05299/K15022/K14138/ MF0093 homoacetogenesis K00196/K00198/K03518/K03519/K03520 MF0094 hydrogen metabolism K00436/K00533/K00534/K06441 MF0095 NADH:ferredoxin oxidoreductase K00529 MF0098 methanogenesis from carbon dioxide K00672/K01499/K00202/K11261/K00441 MF0099 methanol conversion K14080 MF0100 Sulfate reduction (dissimilatory) K00955/K00957/K00956/K00394/K00395/K11180/K11181 MF0101 Sulfate reduction (assimilatory) K00390/K00860/K00955/K00957/K00956/K00380/K00381 K01186/K05970/K01132/K01135/K01137/K01205/K01207/ MF0102 mucin degradation K12373/K01227/K13714/K01206 MF0103 nitrate reduction (assimilatory) K00366/K01915/K00262/K00362 MF0104 nitrate reduction (dissimilatory) K03385 K00368/K00370/K00371/K00374/K00373/K02567/K02568/ MF0105 nitrate reduction (denitrification) K04561 MF0106 anaerobic fatty acid beta-oxidation K06076/K12507/K06445/K00632/K01782 MF0107 glycerol degradation (propanediol pathway) K00086/K06120/K06121 MF0108 glycerol degradation (dihydroxyacetone pathway) K00005/K00863/K01803 MF0109 glycerol degradation (glycerol kinase pathway) K00864/K01126/K00111/K01803/K00112/K00113 MF0110 glyoxylate bypass K01647/K01681/K01682/K01637/K00024/K01596/K01610 MF0111 triacylglycerol degradation K01046 MF0112 acetate to acetyl-CoA K01895 MF0113 acetyl-CoA to acetate K01905/K01067/K00625/K00925 MF0114 acetyl-CoA to crotonyl-CoA K00626/K00023/K01782/K01825/K01715/K01692 MF0115 Crotonyl-coA from succinate K14534/K01902/K01903 MF0116 butyrate production via transferase K00248/K01034/K01035 MF0117 butyrate production via kinase K00248/K00634/K00929 MF0118 formate conversion K05299/K00123/K00124/K00125/K00127/K08348/K08350 MF0119 lactate production K00016/K03777/K03778 MF0120 lactate consumption K00101/K00102 MF0121 propionate production (acrylate pathway) K01026/K00249 MF0122 propionate production (succinate pathway) K01847/K01849/K01848/K05606/K01902/K01903 MF0123 propionate production (propanediol pathway) K00048/K01699/K13919/K13920/K00086/K13922/K13921 MF0124 Fucose degradation K01818/K00879/K01628/K01803 MF0125 propionate production via kinase K13788/K13923/K00932 MF0126 propionate production via transferase K01026 K01596/K01610/K00024/K00116/K01676/K01679/K00873/ MF0127 Succinate production K01958/K01960/K01677/K01678/K00239/K00240/K00241/ K00242/K00244/K00245/K00246/K00247 MF0128 Propionate conversion to succinate K01659/K01720/K01682/K03417 MF0129 catalase K03781/K03782 K00428/K03782/K00432/K00433/K03386/K03564/K11065/ MF0130 peroxidase K07223 MF0131 superoxide dismutase K04564/K04565 MF0132 superoxide reductase K05919 K02523/K00805/K02548/K02551/K08680/K02549/K01911/ MF0133 menaquinone production K01661/K02361/K02552/K11782/K11783/K11784/K11785 M00791 Manganese/zinc transport system K10830/K19971/K19972 M00319 Manganese/zinc/iron transport system K11707/K11708/K11709/K11710 M00241 Vitamin B12 transport system K06073/K06858 M00586 Putative amino-acid transport system K16961/K16962/K16963 M00223 Phosphonate transport system K02041/K02042/K02044 Thiamine biosynthesis, AIR => thiamine- M00127 K00788/K00878/K00941/K00946/K03147/K14153 P/thiamine-2P GABA biosynthesis, eukaryotes, putrescine => M00135 K00128/K00274/K00657