| Condition | Gene | Description | Fitness | Cons. |
|---|
| 2,6-diaminopimelic acid | Atu0946 | dehydrogenase | -2.4 | |
| 2,6-diaminopimelic acid | Atu0947 | transcriptional regulator, AsnC family | -1.7 | |
| 2,6-diaminopimelic acid | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -3.3 | |
| 2,6-diaminopimelic acid | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -2.0 | |
| 2,6-diaminopimelic acid | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -2.3 | |
| 2,6-diaminopimelic acid | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -2.2 | |
| 2,6-diaminopimelic acid | Atu2128 | acetolactate synthase large subunit | -1.1 | |
| 2,6-diaminopimelic acid | Atu4153 | aldehyde dehydrogenase | -1.8 | |
| 2,6-diaminopimelic acid | Atu8135 | hypothetical protein | +1.8 | |
| 3-aminobutyric acid | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -2.3 | |
| 3-aminobutyric acid | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -2.1 | |
| 3-aminobutyric acid | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -2.0 | |
| 3-aminobutyric acid | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -2.3 | |
| 3-aminobutyric acid | Atu3291 | Lpr family transcriptional regulator | -2.7 | |
| 3-aminobutyric acid | Atu3292 | alanine racemase | -2.2 | |
| 3-aminobutyric acid | Atu3293 | D-amino acid dehydrogenase small subunit | -3.4 | |
| 3-aminobutyric acid | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.9 | |
| 3-aminobutyric acid | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -2.1 | |
| 3-aminobutyric acid | Atu3298 | C4-dicarboxylate transporter DctA | -1.9 | |
| 3-aminobutyric acid | Atu3328 | aldehyde dehydrogenase | -2.9 | |
| 3-aminobutyric acid | Atu3329 | beta alanine--pyruvate transaminase | -3.2 | Yes |
| 3-aminobutyric acid | Atu3913 | biotin carboxylase | -1.4 | |
| 4-Aminobutyric acid | Atu1444 | nitrogen regulation protein | -1.7 | |
| 4-Aminobutyric acid | Atu2422 | ABC transporter, substrate binding protein (amino acid) | -2.5 | |
| 4-Aminobutyric acid | Atu2424 | ABC transporter, nucleotide binding/ATPase protein | -3.2 | |
| 4-Aminobutyric acid | Atu2425 | ABC transporter, nucleotide binding/ATPase protein | -3.0 | |
| 4-Aminobutyric acid | Atu2426 | ABC transporter, membrane spanning protein (branched chain amino acid) | -3.2 | |
| 4-Aminobutyric acid | Atu2427 | ABC transporter, membrane spanning protein | -3.1 | |
| 4-Aminobutyric acid | Atu3291 | Lpr family transcriptional regulator | -3.9 | |
| 4-Aminobutyric acid | Atu3292 | alanine racemase | -2.3 | |
| 4-Aminobutyric acid | Atu3293 | D-amino acid dehydrogenase small subunit | -4.2 | |
| 4-Aminobutyric acid | Atu5483 | GntR family transcriptional regulator | +1.2 | |
| 5-Aminolevulinic acid | Atu3300 | aminotransferase | -1.2 | |
| 5-Aminolevulinic acid | Atu3301 | short-chain alcohol dehydrogenase | -1.4 | |
| 5-Aminolevulinic acid | Atu3906 | nitrate ABC transporter ATPase | +1.7 | |
| 5-Aminolevulinic acid | Atu4018 | two component sensor kinase | -1.7 | |
| 5-Aminolevulinic acid | Atu4019 | two component response regulator | -1.6 | |
| 5-Aminovaleric acid | Atu2424 | ABC transporter, nucleotide binding/ATPase protein | -1.3 | |
| 5-Aminovaleric acid | Atu3293 | D-amino acid dehydrogenase small subunit | -2.7 | |
| 5-Aminovaleric acid | Atu3300 | aminotransferase | -1.8 | |
| 5-Aminovaleric acid | Atu3301 | short-chain alcohol dehydrogenase | -1.8 | |
| 5-Aminovaleric acid | Atu3397 | hypothetical protein | +1.5 | |
| 5-Aminovaleric acid | Atu4419 | LysR family transcriptional regulator | -1.3 | |
| 5-Aminovaleric acid | Atu5122 | 3-ketoacyl-ACP reductase | +1.1 | |
| Ammonium chloride | Atu3296 | two component response regulator for C4-dicarboxylate transport | -2.3 | |
| Ammonium chloride | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -2.1 | |
| Ammonium chloride | Atu3298 | C4-dicarboxylate transporter DctA | -2.0 | |
| Beta-alanine | Atu0207 | transcriptional regulator, LysR family | -2.9 | |
| Beta-alanine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -2.5 | |
| Beta-alanine | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -1.5 | |
| Beta-alanine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -1.7 | |
| Beta-alanine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -1.7 | |
| Beta-alanine | Atu3291 | Lpr family transcriptional regulator | -4.6 | |
| Beta-alanine | Atu3292 | alanine racemase | -3.1 | |
| Beta-alanine | Atu3293 | D-amino acid dehydrogenase small subunit | -4.1 | Yes |
| Beta-alanine | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.3 | |
| Beta-alanine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.2 | |
| Beta-alanine | Atu3298 | C4-dicarboxylate transporter DctA | -1.4 | |
| Beta-alanine | Atu3328 | aldehyde dehydrogenase | -4.2 | |
| Beta-alanine | Atu3329 | beta alanine--pyruvate transaminase | -3.7 | Yes |
| Betaine | Atu0726 | ring hydroxylating dioxygenase, alpha-subunit | -3.9 | Yes |
| Betaine | Atu0727 | ferredoxin I | -3.5 | Yes |
| Betaine | Atu1632 | dimethylglycine dehydrogenase | -3.7 | |
| Betaine | Atu1670 | alcohol dehydrogenase class III | -1.1 | Yes |
| Betaine | Atu1759 | L-serine dehydratase | -3.1 | |
| Betaine | Atu1767 | transcriptional regulator, AraC family | -3.0 | Yes |
| Betaine | Atu4309 | AraC family transcriptional regulator | -1.4 | |
| Betaine | Atu4310 | sarcosine oxidase beta subunit | -1.6 | |
| Betaine | Atu4311 | sarcosine oxidase delta subunit | -1.4 | Yes |
| Betaine | Atu4312 | sarcosine oxidase alpha subunit | -1.6 | Yes |
| Betaine | Atu4313 | sarcosine oxidase gamma subunit | -1.6 | |
| Carnitine Hydrochloride | Atu3906 | nitrate ABC transporter ATPase | +2.5 | |
| Choline chloride | Atu0726 | ring hydroxylating dioxygenase, alpha-subunit | -3.4 | Yes |
| Choline chloride | Atu0727 | ferredoxin I | -3.2 | Yes |
| Choline chloride | Atu0781 | hypothetical protein | +3.9 | |
| Choline chloride | Atu0828 | transcriptional regulator BetI | -2.8 | |
| Choline chloride | Atu0829 | betaine aldehyde dehydrogenase | -2.9 | |
| Choline chloride | Atu0830 | choline dehydrogenase | -2.9 | Yes |
| Choline chloride | Atu1444 | nitrogen regulation protein | -2.1 | |
| Choline chloride | Atu1632 | dimethylglycine dehydrogenase | -3.4 | |
| Choline chloride | Atu1759 | L-serine dehydratase | -2.0 | |
| Choline chloride | Atu1767 | transcriptional regulator, AraC family | -2.9 | Yes |
| Choline chloride | Atu2059 | transcriptional regulator, TetR family | +3.1 | |
| Choline chloride | Atu2279 | ABC transporter, nucleotide binding/ATPase protein (proline/glycine betaine) | -2.9 | |
| Choline chloride | Atu2280 | ABC transporter, membrane spanning protein (proline/glycine betaine) | -2.7 | |
| Choline chloride | Atu2281 | ABC transporter, substrate binding protein (proline/glycine betaine) | -3.0 | |
| Choline chloride | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.4 | |
| Choline chloride | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.3 | |
| Choline chloride | Atu3298 | C4-dicarboxylate transporter DctA | -1.4 | |
| Choline chloride | Atu3799 | GntR family transcriptional regulator | +3.0 | |
| D-Alanine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -2.3 | Yes |
| D-Alanine | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -2.1 | Yes |
| D-Alanine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -2.1 | Yes |
| D-Alanine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -2.3 | Yes |
| D-Alanine | Atu3291 | Lpr family transcriptional regulator | -3.8 | |
| D-Alanine | Atu3292 | alanine racemase | -3.1 | Yes |
| D-Alanine | Atu3293 | D-amino acid dehydrogenase small subunit | -4.6 | Yes |
| D-Alanine | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.5 | |
| D-Alanine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.3 | |
| D-Alanine | Atu3298 | C4-dicarboxylate transporter DctA | -1.4 | |
| D-Alanine | Atu4018 | two component sensor kinase | -3.1 | |
| D-Alanine | Atu4019 | two component response regulator | -3.9 | |
| D-Glucosamine Hydrochloride | Atu3296 | two component response regulator for C4-dicarboxylate transport | +2.3 | |
| D-Glucosamine Hydrochloride | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | +1.8 | |
| D-Glucosamine Hydrochloride | Atu3298 | C4-dicarboxylate transporter DctA | +2.3 | |
| D-Glucosamine Hydrochloride | Atu3342 | trehalose utilization-like protein | +1.6 | |
| D-Glucosamine Hydrochloride | Atu3343 | trehalose utilization-like protein | +2.2 | |
| D-Glucosamine Hydrochloride | Atu3577 | transcriptional regulator | +2.1 | |
| D-Glucosamine Hydrochloride | Atu3906 | nitrate ABC transporter ATPase | +1.2 | |
| D-Lysine | Atu0609 | ABC transporter, substrate binding protein (putrescine) | +1.3 | |
| D-Lysine | Atu0610 | ABC transporter, nucleotide binding/ATPase protein | +1.3 | |
| D-Lysine | Atu0611 | ABC transporter, membrane spanning protein | +1.1 | |
| D-Lysine | Atu0612 | ABC transporter, membrane spanning protein | +1.4 | |
| D-Lysine | Atu0649 | cyclopropane-fatty-acyl-phospholipid synthase | -2.4 | |
| D-Lysine | Atu0654 | transcriptional regulator, LysR family | -1.0 | |
| D-Lysine | Atu1159 | arginine-tRNA-protein transferase | -1.7 | |
| D-Lysine | Atu3292 | alanine racemase | -1.1 | |
| D-Lysine | Atu4018 | two component sensor kinase | -1.5 | |
| D-Lysine | Atu4019 | two component response regulator | -1.6 | |
| D-Lysine | Atu5007 | santhopine-responsive transcriptional repressor | -1.5 | |
| D-Lysine | Atu5483 | GntR family transcriptional regulator | +7.1 | |
| DL-2-Aminobutyric acid | Atu0211 | hypothetical protein | +4.6 | |
| DL-2-Aminobutyric acid | Atu0251 | hypothetical protein | +3.2 | |
| DL-2-Aminobutyric acid | Atu0430 | chaperonin (heat shock protein hsp33) | +1.8 | |
| DL-2-Aminobutyric acid | Atu0498 | hypothetical protein | +1.8 | |
| DL-2-Aminobutyric acid | Atu0535 | hypothetical protein | +2.8 | |
| DL-2-Aminobutyric acid | Atu0984 | aminopeptidase N | +4.3 | |
| DL-2-Aminobutyric acid | Atu1287 | hypothetical protein | +3.2 | |
| DL-2-Aminobutyric acid | Atu1329 | leucyl/phenylalanyl-tRNA-protein transferase | +2.5 | |
| DL-2-Aminobutyric acid | Atu1490 | arsenate reductase | +3.8 | |
| DL-2-Aminobutyric acid | Atu1577 | ABC transporter, substrate binding protein (amino acid) | +10.3 | |
| DL-2-Aminobutyric acid | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | +10.5 | |
| DL-2-Aminobutyric acid | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | +9.5 | |
| DL-2-Aminobutyric acid | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | +10.6 | |
| DL-2-Aminobutyric acid | Atu1759 | L-serine dehydratase | +8.3 | |
| DL-2-Aminobutyric acid | Atu2184 | transcriptional regulator, AsnC family | +7.9 | |
| DL-2-Aminobutyric acid | Atu2333 | ATP-dependent RNA helicase | +2.9 | |
| DL-2-Aminobutyric acid | Atu2378 | hypothetical protein | +3.6 | |
| DL-2-Aminobutyric acid | Atu2424 | ABC transporter, nucleotide binding/ATPase protein | +6.4 | |
| DL-2-Aminobutyric acid | Atu2425 | ABC transporter, nucleotide binding/ATPase protein | +6.2 | |
| DL-2-Aminobutyric acid | Atu2426 | ABC transporter, membrane spanning protein (branched chain amino acid) | +7.0 | |
| DL-2-Aminobutyric acid | Atu2427 | ABC transporter, membrane spanning protein | +7.2 | |
| DL-2-Aminobutyric acid | Atu2485 | hypothetical protein | +1.8 | |
| DL-2-Aminobutyric acid | Atu3760 | hypothetical protein | +4.4 | |
| DL-2-Aminobutyric acid | Atu3792 | L-asparagine permease | +10.1 | |
| DL-2-Aminobutyric acid | Atu3884 | hypothetical protein | +6.2 | |
| DL-2-Aminobutyric acid | Atu8130 | hypothetical protein | +2.5 | |
| DL-2-Aminobutyric acid | Atu8177 | hypothetical protein | +2.1 | |
| Ethanolamine | Atu2138 | dehydrogenase | -2.8 | |
| Ethanolamine | Atu2139 | aldehyde dehydrogenase | -2.8 | |
| Ethanolamine | Atu2140 | hypothetical protein | -3.4 | |
| Ethanolamine | Atu2141 | hypothetical protein | -2.6 | |
| Ethanolamine | Atu2142 | glutamine synthetase | -2.5 | |
| Ethanolamine | Atu2143 | ABC transporter, membrane spanning protein (amino acid) | -2.4 | |
| Ethanolamine | Atu2144 | hypothetical protein | -2.8 | |
| Ethanolamine | Atu2428 | exopolysaccharide production protein PssB | -1.2 | |
| Glycine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -1.6 | |
| Glycine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -1.3 | |
| Glycine | Atu1759 | L-serine dehydratase | -2.2 | Yes |
| Glycine | Atu2131 | hypothetical protein | -1.1 | |
| Glycine | Atu2416 | glutamine synthetase | -1.2 | |
| Glycine | Atu4018 | two component sensor kinase | -1.9 | |
| Glycine | Atu4019 | two component response regulator | -1.7 | |
| Hydantoin | Atu0079 | Atu0079-1 mutant of pfkB family carbohydrate kinase | -2.3 | |
| Hydantoin | Atu0272 | transcriptional regulator, MarR family | +3.0 | |
| Hydantoin | Atu1770 | glutamine synthetase | -1.2 | |
| Hydantoin | Atu2386 | dihydropyrimidinase | +2.1 | |
| Hydantoin | Atu2757 | nitrogen regulatory protein PII | -1.0 | |
| Hydantoin | Atu2758 | ammonium transporter | -1.1 | |
| Hydantoin | Atu8135 | hypothetical protein | +1.2 | |
| L-Alanine | Atu3291 | Lpr family transcriptional regulator | -4.1 | |
| L-Alanine | Atu3292 | alanine racemase | -3.8 | Yes |
| L-Alanine | Atu3293 | D-amino acid dehydrogenase small subunit | -4.5 | Yes |
| L-Alanine | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.4 | |
| L-Alanine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.5 | |
| L-Alanine | Atu3298 | C4-dicarboxylate transporter DctA | -1.6 | |
| L-Arginine | Atu0654 | transcriptional regulator, LysR family | -1.1 | |
| L-Arginine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -1.2 | |
| L-Arginine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -1.7 | |
| L-Arginine | Atu2396 | urease accessory protein | -3.7 | Yes |
| L-Arginine | Atu2397 | urease accessory protein | -3.3 | |
| L-Arginine | Atu2398 | urease accessory protein | -2.3 | |
| L-Arginine | Atu2401 | urease alpha subunit | -3.0 | Yes |
| L-Arginine | Atu2404 | hypothetical protein | -2.1 | |
| L-Arginine | Atu2407 | urease gamma subunit | -3.2 | |
| L-Arginine | Atu2408 | urease accessory protein | -3.3 | |
| L-Arginine | Atu3296 | two component response regulator for C4-dicarboxylate transport | -2.1 | |
| L-Arginine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.8 | |
| L-Arginine | Atu3298 | C4-dicarboxylate transporter DctA | -2.0 | |
| L-Arginine | Atu3300 | aminotransferase | -1.0 | |
| L-Arginine | Atu4007 | arginase | -3.3 | Yes |
| L-Asparagine | Atu3791 | L-asparaginase | -1.5 | Yes |
| L-Aspartic Acid | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -2.5 | Yes |
| L-Aspartic Acid | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -2.7 | Yes |
| L-Aspartic Acid | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -2.9 | Yes |
| L-Aspartic Acid | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -2.5 | |
| L-Aspartic Acid | Atu3791 | L-asparaginase | +2.1 | |
| L-Aspartic Acid | Atu3792 | L-asparagine permease | +1.7 | |
| L-Cysteine hydrochloride monohydrate | Atu0251 | hypothetical protein | -2.6 | |
| L-Cysteine hydrochloride monohydrate | Atu3296 | two component response regulator for C4-dicarboxylate transport | -2.3 | |
| L-Cysteine hydrochloride monohydrate | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -2.2 | |
| L-Cysteine hydrochloride monohydrate | Atu3298 | C4-dicarboxylate transporter DctA | -2.4 | |
| L-Cysteine hydrochloride monohydrate | Atu4081 | aspartate racemase | -4.7 | |
| L-Cysteine hydrochloride monohydrate | Atu4082 | AsnC family transcriptional regulator | -4.4 | |
| L-Cysteine hydrochloride monohydrate | Atu4089 | ABC transporter permease | -6.0 | |
| L-Cysteine hydrochloride monohydrate | Atu4090 | ABC transporter permease | -5.0 | |
| L-Cysteine hydrochloride monohydrate | Atu4091 | cytochrome d oxidase | -5.0 | |
| L-Cysteine hydrochloride monohydrate | Atu4092 | cytochrome d oxidase subunit II | -5.7 | |
| L-Cysteine hydrochloride monohydrate | Atu8036 | protein YBGT-like protein | -6.3 | |
| L-Glutamic acid monopotassium salt monohydrate | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -3.0 | Yes |
| L-Glutamic acid monopotassium salt monohydrate | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -3.1 | Yes |
| L-Glutamic acid monopotassium salt monohydrate | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -4.0 | Yes |
| L-Glutamic acid monopotassium salt monohydrate | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -3.3 | |
| L-Glutamic acid monopotassium salt monohydrate | Atu2766 | NAD-glutamate dehydrogenase | -1.8 | |
| L-Glutamine | Atu0291 | hypothetical protein | -1.8 | |
| L-Glutamine | Atu4498 | hypothetical protein | -1.4 | |
| L-Histidine | Atu0291 | hypothetical protein | -2.4 | |
| L-Histidine | Atu0804 | proton/glutamate transport protein | +1.3 | |
| L-Histidine | Atu1372 | hypothetical protein | -1.5 | |
| L-Histidine | Atu1572 | hydrolase | -1.9 | |
| L-Histidine | Atu1759 | L-serine dehydratase | +1.8 | |
| L-Histidine | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.4 | |
| L-Histidine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.3 | |
| L-Histidine | Atu3298 | C4-dicarboxylate transporter DctA | -1.5 | |
| L-Histidine | Atu3792 | L-asparagine permease | +1.7 | Yes |
| L-Histidine | Atu3931 | urocanate hydratase | -2.1 | Yes |
| L-Histidine | Atu3932 | hypothetical protein | -2.2 | Yes |
| L-Histidine | Atu3933 | histidine ammonia-lyase | -3.2 | Yes |
| L-Histidine | Atu3934 | imidazolonepropionase | -3.4 | Yes |
| L-Histidine | Atu3935 | N-formimino-L-glutamate deiminase | -4.8 | Yes |
| L-Histidine | Atu3936 | GntR family transcriptional regulator | +1.6 | |
| L-Isoleucine | Atu0490 | hypothetical protein | -1.2 | |
| L-Isoleucine | Atu0871 | branched-chain-amino-acid aminotransferase | -1.3 | Yes |
| L-Isoleucine | Atu3906 | nitrate ABC transporter ATPase | +1.1 | |
| L-Leucine | Atu0871 | branched-chain-amino-acid aminotransferase | -2.4 | Yes |
| L-Leucine | Atu1442 | competence/damage-inducible protein CinA | -1.9 | |
| L-Leucine | Atu1770 | glutamine synthetase | -1.3 | |
| L-Leucine | Atu2023 | NADH dehydrogenase | -1.1 | |
| L-Leucine | Atu2425 | ABC transporter, nucleotide binding/ATPase protein | -1.1 | Yes |
| L-Leucine | Atu2427 | ABC transporter, membrane spanning protein | -1.2 | Yes |
| L-Leucine | Atu2428 | exopolysaccharide production protein PssB | -2.2 | |
| L-Leucine | Atu3293 | D-amino acid dehydrogenase small subunit | -1.4 | Yes |
| L-Leucine | Atu4018 | two component sensor kinase | -3.8 | |
| L-Leucine | Atu4019 | two component response regulator | -3.4 | |
| L-Lysine | Atu0946 | dehydrogenase | -3.1 | Yes |
| L-Lysine | Atu0947 | transcriptional regulator, AsnC family | -3.0 | Yes |
| L-Lysine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -1.9 | Yes |
| L-Lysine | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -1.6 | |
| L-Lysine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -1.8 | |
| L-Lysine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -2.3 | Yes |
| L-Lysine | Atu2128 | acetolactate synthase large subunit | -1.3 | |
| L-Lysine | Atu2769 | acetyl-CoA acetyltransferase; poly-beta-hydroxybutyrate biosynthesis | -3.0 | Yes |
| L-Lysine | Atu3597 | 3-hydroxybutyryl-CoA dehydrogenase | -1.7 | |
| L-Lysine | Atu4151 | LysR family transcriptional regulator | -2.0 | |
| L-Lysine | Atu4153 | aldehyde dehydrogenase | -2.6 | Yes |
| L-Lysine | Atu4419 | LysR family transcriptional regulator | -1.3 | Yes |
| L-Methionine | Atu0654 | transcriptional regulator, LysR family | -1.2 | |
| L-Methionine | Atu0871 | branched-chain-amino-acid aminotransferase | -1.1 | |
| L-Methionine | Atu2035 | acetolactate synthase, small subunit | -1.2 | |
| L-Ornithine | Atu0654 | transcriptional regulator, LysR family | -2.8 | |
| L-Ornithine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | +1.3 | |
| L-Ornithine | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | +1.3 | |
| L-Ornithine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | +1.2 | |
| L-Ornithine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | +1.5 | |
| L-Ornithine | Atu2397 | urease accessory protein | -1.7 | |
| L-Ornithine | Atu2401 | urease alpha subunit | -1.7 | |
| L-Ornithine | Atu2408 | urease accessory protein | -1.6 | |
| L-Ornithine | Atu2758 | ammonium transporter | -1.2 | |
| L-Ornithine | Atu2783 | acetyltransferase | -2.4 | |
| L-Ornithine | Atu3300 | aminotransferase | -2.8 | |
| L-Ornithine | Atu3301 | short-chain alcohol dehydrogenase | -1.4 | |
| L-Ornithine | Atu4007 | arginase | -1.0 | |
| L-Ornithine | Atu8135 | hypothetical protein | -2.6 | |
| L-Phenylalanine | Atu0529 | aspartate transaminase | -1.1 | |
| L-Phenylalanine | Atu2425 | ABC transporter, nucleotide binding/ATPase protein | -1.2 | |
| L-Phenylalanine | Atu2427 | ABC transporter, membrane spanning protein | -1.3 | |
| L-Phenylalanine | Atu4226 | transcriptional regulator | -1.2 | |
| L-Phenylalanine | Atu5007 | santhopine-responsive transcriptional repressor | +1.4 | |
| L-Phenylalanine | Atu8135 | hypothetical protein | +1.8 | |
| L-Pipecolic Acid | Atu0807 | metallo-beta-lactamase superfamily protein | -1.2 | |
| L-Pipecolic Acid | Atu1867 | glutamate racemase | +1.4 | |
| L-Pipecolic Acid | Atu2128 | acetolactate synthase large subunit | -1.9 | |
| L-Pipecolic Acid | Atu2559 | transcriptional regulator, LysR family | -1.6 | |
| L-Pipecolic Acid | Atu2560 | oxidoreductase | -2.5 | Yes |
| L-Pipecolic Acid | Atu2769 | acetyl-CoA acetyltransferase; poly-beta-hydroxybutyrate biosynthesis | -1.9 | |
| L-Pipecolic Acid | Atu3597 | 3-hydroxybutyryl-CoA dehydrogenase | -1.5 | |
| L-Pipecolic Acid | Atu4151 | LysR family transcriptional regulator | -2.4 | |
| L-Pipecolic Acid | Atu4153 | aldehyde dehydrogenase | -2.9 | Yes |
| L-Pipecolic Acid | Atu4419 | LysR family transcriptional regulator | -2.1 | |
| L-Pipecolic Acid | Atu4477 | TetR family transcriptional regulator | -1.4 | |
| L-Proline | Atu1444 | nitrogen regulation protein | -1.4 | |
| L-Proline | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -3.5 | |
| L-Proline | Atu1578 | ABC transporter, membrane spanning protein (amino acid) | -2.9 | |
| L-Proline | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -2.4 | |
| L-Proline | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -3.1 | |
| L-Proline | Atu2424 | ABC transporter, nucleotide binding/ATPase protein | -1.4 | Yes |
| L-Proline | Atu2425 | ABC transporter, nucleotide binding/ATPase protein | -1.1 | Yes |
| L-Proline | Atu2426 | ABC transporter, membrane spanning protein (branched chain amino acid) | -1.1 | |
| L-Proline | Atu2766 | NAD-glutamate dehydrogenase | -1.9 | |
| L-Proline | Atu4157 | bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase | -4.9 | Yes |
| L-Proline | Atu4159 | AsnC family transcriptional regulator | -4.7 | Yes |
| L-Pyroglutamic acid | Atu0251 | hypothetical protein | -1.5 | |
| L-Pyroglutamic acid | Atu2428 | exopolysaccharide production protein PssB | -3.8 | |
| L-Pyroglutamic acid | Atu2766 | NAD-glutamate dehydrogenase | -2.6 | |
| L-Pyroglutamic acid | Atu3909 | hypothetical protein | -3.9 | |
| L-Pyroglutamic acid | Atu3911 | hypothetical protein | -3.7 | |
| L-Pyroglutamic acid | Atu3912 | hypothetical protein | -3.7 | |
| L-Pyroglutamic acid | Atu3913 | biotin carboxylase | -3.5 | |
| L-Pyroglutamic acid | Atu4018 | two component sensor kinase | -3.1 | |
| L-Pyroglutamic acid | Atu4019 | two component response regulator | -2.9 | |
| L-Serine | Atu1577 | ABC transporter, substrate binding protein (amino acid) | -1.5 | Yes |
| L-Serine | Atu1579 | ABC transporter, membrane spanning protein (amino acid) | -1.4 | Yes |
| L-Serine | Atu1580 | ABC transporter, nucleotide binding/ATPase protein (amino acid) | -1.4 | |
| L-Serine | Atu1759 | L-serine dehydratase | -3.1 | Yes |
| L-Serine | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.2 | |
| L-Serine | Atu3298 | C4-dicarboxylate transporter DctA | -1.6 | |
| L-Threonine | Atu1759 | L-serine dehydratase | -1.4 | |
| L-Threonine | Atu1764 | methylenetetrahydrofolate reductase | -1.1 | |
| L-Threonine | Atu2131 | hypothetical protein | -1.3 | |
| L-Threonine | Atu2184 | transcriptional regulator, AsnC family | -1.6 | |
| L-Threonine | Atu2416 | glutamine synthetase | -1.5 | |
| L-Threonine | Atu2758 | ammonium transporter | -1.0 | Yes |
| L-Threonine | Atu3785 | threonine aldolase | -3.3 | Yes |
| L-Valine | Atu0490 | hypothetical protein | -1.9 | |
| L-Valine | Atu0498 | hypothetical protein | -1.3 | |
| L-Valine | Atu0871 | branched-chain-amino-acid aminotransferase | -2.9 | Yes |
| L-Valine | Atu5122 | 3-ketoacyl-ACP reductase | +1.1 | |
| L-Valine | Atu5483 | GntR family transcriptional regulator | +1.3 | |
| L-Valine | Atu8135 | hypothetical protein | -1.5 | |
| N-Acetyl-D-Glucosamine | Atu0790 | hypothetical protein | -2.0 | |
| N-Acetyl-D-Glucosamine | Atu1444 | nitrogen regulation protein | -2.3 | |
| N-Acetyl-D-Glucosamine | Atu2598 | transcriptional regulator, RpiR family | +2.0 | Yes |
| N-Acetyl-D-Glucosamine | Atu2600 | ABC transporter, nucleotide binding/ATPase protein (maltose/maltodextrin) | -4.1 | |
| N-Acetyl-D-Glucosamine | Atu2601 | ABC transporter, substrate binding protein (maltose) | -4.4 | |
| N-Acetyl-D-Glucosamine | Atu2602 | ABC transporter, membrane spanning protein (maltose) | -3.8 | |
| N-Acetyl-D-Glucosamine | Atu2603 | ABC transporter, membrane spanning protein (maltose) | -4.3 | |
| N-Acetyl-D-Glucosamine | Atu2604 | oxidoreductase | -4.4 | |
| N-Acetyl-D-Glucosamine | Atu2606 | transcriptional regulator, GntR family | -4.2 | |
| N-Acetyl-D-Glucosamine | Atu2607 | glucosamine--fructose-6-phosphate aminotransferase | -3.5 | Yes |
| N-Acetyl-D-Glucosamine | Atu2608 | N-acetylglucosamine-6-phosphate deacetylase | -3.6 | Yes |
| N-Acetyl-D-Glucosamine | Atu2609 | transcriptional regulator, ROK family | -5.4 | |
| Nicotinamide | Atu2066 | pyrazinamidase/nicotinamidase | -2.7 | |
| Orotic acid | Atu0272 | transcriptional regulator, MarR family | -2.1 | |
| Orotic acid | Atu0372 | hypothetical protein | -1.4 | |
| Orotic acid | Atu1624 | transcriptional regulator, TetR family | -1.3 | |
| Orotic acid | Atu2328 | hypothetical protein | -1.4 | |
| Orotic acid | Atu2496 | nitroreducatase | -2.2 | |
| Orotic acid | Atu2497 | hydrolase | -2.1 | |
| Orotic acid | Atu2498 | hypothetical protein | -2.2 | |
| Orotic acid | Atu2499 | Isochorismatase | -2.5 | |
| Orotic acid | Atu2500 | monooxygenase (pyrimidine utilization protein A) | -3.0 | |
| Orotic acid | Atu2757 | nitrogen regulatory protein PII | -1.5 | |
| Orotic acid | Atu3294 | GntR family transcriptional regulator | -1.5 | |
| Orotic acid | Atu3296 | two component response regulator for C4-dicarboxylate transport | -1.3 | |
| Orotic acid | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -1.4 | |
| Orotic acid | Atu3298 | C4-dicarboxylate transporter DctA | -1.3 | |
| Orotic acid | Atu4530 | TetR family transcriptional regulator | -2.3 | |
| Orotic acid | Atu4702 | GntR family transcriptional regulator | -2.0 | |
| Putrescine Dihydrochloride | Atu0194 | oxidoreductase | -1.1 | Yes |
| Putrescine Dihydrochloride | Atu0609 | ABC transporter, substrate binding protein (putrescine) | -1.3 | Yes |
| Putrescine Dihydrochloride | Atu0610 | ABC transporter, nucleotide binding/ATPase protein | -1.4 | Yes |
| Putrescine Dihydrochloride | Atu0611 | ABC transporter, membrane spanning protein | -1.5 | Yes |
| Putrescine Dihydrochloride | Atu3906 | nitrate ABC transporter ATPase | +1.6 | |
| Putrescine Dihydrochloride | Atu5123 | acetolactate synthase catalytic subunit | +1.2 | |
| Sodium nitrate | Atu0671 | hypothetical protein | -1.6 | Yes |
| Sodium nitrate | Atu1444 | nitrogen regulation protein | -1.8 | |
| Sodium nitrate | Atu3296 | two component response regulator for C4-dicarboxylate transport | -2.4 | |
| Sodium nitrate | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -2.1 | |
| Sodium nitrate | Atu3298 | C4-dicarboxylate transporter DctA | -2.1 | |
| Sodium nitrate | Atu3901 | nitrite reductase small subunit | -3.0 | Yes |
| Sodium nitrate | Atu3902 | nitrite reductase large subunit | -3.0 | Yes |
| Sodium nitrate | Atu3903 | nitrate ABC transporter ATPase | -2.6 | Yes |
| Sodium nitrate | Atu3904 | nitrate ABC transporter permease | -2.9 | |
| Sodium nitrate | Atu3905 | nitrate ABC transporter substrate-binding protein | -3.0 | Yes |
| Sodium nitrate | Atu3907 | two component response regulator | -2.9 | Yes |
| Sodium nitrate | Atu4530 | TetR family transcriptional regulator | +1.5 | |
| Urea | Atu3296 | two component response regulator for C4-dicarboxylate transport | -2.4 | |
| Urea | Atu3297 | two component sensor kinase for C4-dicarboxylate transport | -2.1 | |
| Urea | Atu3298 | C4-dicarboxylate transporter DctA | -2.3 | |
| e-Amino-N-Caproic Acid | Atu3293 | D-amino acid dehydrogenase small subunit | -2.2 | |
| e-Amino-N-Caproic Acid | Atu3300 | aminotransferase | -1.7 | |
| e-Amino-N-Caproic Acid | Atu3301 | short-chain alcohol dehydrogenase | -1.2 | |
| e-Amino-N-Caproic Acid | Atu5122 | 3-ketoacyl-ACP reductase | +2.0 | |
| e-Amino-N-Caproic Acid | Atu5123 | acetolactate synthase catalytic subunit | +2.1 | |
| spermidine | Atu0194 | oxidoreductase | -1.0 | |
| spermidine | Atu0609 | ABC transporter, substrate binding protein (putrescine) | -1.3 | |
| spermidine | Atu0610 | ABC transporter, nucleotide binding/ATPase protein | -1.6 | Yes |
| spermidine | Atu0611 | ABC transporter, membrane spanning protein | -1.9 | Yes |
| spermidine | Atu3293 | D-amino acid dehydrogenase small subunit | -1.5 | |
| spermidine | Atu3369 | hypothetical protein | -2.0 | |
| spermidine | Atu5122 | 3-ketoacyl-ACP reductase | +1.7 | |
| spermidine | Atu5124 | glutamate-1-semialdehyde aminotransferase | -1.4 | |