Table 1.
Primer and probe sequences used in this study.
| Probe name | Sequence (5'-3') | Position/Modification |
| ilvA | ||
| Forward primer | TGTCGTCGCGTCTTGATAAC | 119 |
| Reverse primer | TTCGTCGTGGCAATCGTAGC | 1506c |
| Helper probe 1 | GGAAGGTTTCGTCACCGATG | 757c |
| Detection probe | GTCGAGATACTCCTGGCATA | 780c [3' DIG tail] |
| Capture probe | TCGCTATCGACGGTGATGAT | 803c [5' biotin] |
| Helper probe 2 | TCCTTCATCGCCGCACAGAT | 827c |
| ilvG | ||
| Forward primer | ACTTGCTATGCCGACATGAG | 122 |
| Reverse primer | GGCCAGACGTTCTCAAGTTC | 1593c |
| Helper probe 1 | CCAGAAAGCTGTGCTTGGTA | 382c |
| Detection probe | CAACTCTTCCAGCGATGCA | 402c [3' DIG tail] |
| Capture probe | AATGCTTCAGCCATGATGCG | 425c [5' biotin] |
| Helper probe 2 | ACGACCTGAGCAGGCAACGT | 447c |
| leuA | ||
| Forward primer | CACATTGCGCGACGGTGAAC | 30 |
| Reverse primer | CTGCGGCACGCCAGATATTG | 1510c |
| Helper probe 1 | TGCTTACCGATGAAGGCCAG | 1151c |
| Detection probe | AATGCTCCGGCTCTTCTTGC | 1171c [3' DIG tail] |
| Capture probe | CGCTGAAGTAATCCAGATGG | 1192c [5' biotin] |
| Helper probe 2 | ATCGTTAGAGCCAGACTGCA | 1212c |
| ilvB | ||
| Forward primer | GCGGTTCTATGCTGCCTGTT | 107 |
| Reverse primer | GCGGATCGGCTTCGTTATTC | 1561c |
| Helper probe 1 | GCGTTGATCAGGCCGTAA | 1127c |
| Detection probe | TCATCGACACAGGCGGCAA | 1148c [3' DIG tail] |
| Capture probe | CGTCGGTGGTGATAATTGCA | 1171c [5' biotin] |
| Helper probe 2 | TCCACATCTGATGCTGACCA | 1192c |
| ilvI | ||
| Forward primer | TTGTCTGGAGCCGAGATGGT | 10 |
| Reverse primer | CATGTCCTGCCACTGCTTCA | 1461c |
| Helper probe 1 | TTGTTCGAGGACCTGGC | 990c |
| Detection probe | GCGGATTCTTGCGACAAG | 1019c [3' DIG tail] |
| Capture probe | CTCATCCAGTGGTTGATG | 1038c [5' biotin] |
| Helper probe 2 | TTGCTGCCACCAGTC | 1059c |
| pflB | ||
| Forward primer | TTCCTGGCTGGCGCTACTGA | 128 |
| Reverse primer | TCCATCGCGTCGAGCAGCAT | 2162c |
| Helper probe 1 | AGGTAGCCGAAGTAAGTCCA | 791c |
| Detection probe | TCTGAGACTTAACAGCAGCC | 811c [3' DIG tail] |
| Capture probe | CGAAGGACATTGCAGCACCG | 832c [5' biotin] |
| Helper probe 2 | CAGGAAGGTGGAGGTACGAC | 852c |
| ldhA | ||
| Forward primer | CTGCAACAGGTGAACGAGTC | 46 |
| Reverse primer | CTGGATCACGTCGTTGGATT | 831c |
| Helper probe 1 | GGCTGGAACACGGACTACTT | 297c |
| Detection probe | CATCATACCGATGGCGTGTT | 339c [3' DIG tail] |
| Capture probe | GCAACGGCCTCTGGATCATA | 317c [5' biotin] |
| Helper probe 2 | AATACGGCGGTTCAGCGTCA | 360c |
| aceA | ||
| Forward primer | CATACAGTGCGGAAGATGTG | 77 |
| Reverse primer | GAACTGCGATTCTTCAGTGG | 1302c |
| Helper probe 1 | ACCACAGCTGGCACCGAGTT | 362c |
| Detection probe | ACCATTGGATCTGATCGGCA | 409c [3' DIG tail] |
| Capture probe | ACGGAAGGTGTTGTTGATCC | 387c [5' biotin] |
| frdA | ||
| Forward primer | GCCGATCTTGCCATTGTAGG | 16 |
| Reverse primer | TGGCGGCAGCGTAGTAATCT | 1728c |
| Helper probe 1 | TTCATTGCTACCAGGCCGCG | 524c |
| Detection probe | CCAGCGTGCCTTCCATCATG | 544c [3' DIG tail] |
| Capture probe | CGCGTTAGCACGGATCTGCA | 564c [5' biotin] |
| Helper probe 2 | CCGCCAGTAGCCATAACGAC | 584c |
| pykF | ||
| Forward primer | GAATCTGCGCAACGTGATGA | 144 |
| Reverse primer | TGTTAGTAGTGCCGCTCGGT | 1390c |
| Helper probe 1 | CCTTCATACGTTACCGCAAC | 335c |
| Detection probe | GCCAACAGACAGGTCAGTAG | 360c [3' DIG tail] |
| Capture probe | GATCAGACCATCGTCAACCA | 390c [5' biotin] |
| Helper probe 2 | CTTCAATGGCGGTAACTTCC | 415c |
| ppc | ||
| Forward primer | GCGCTGGCAATGATGCTAAC | 137 |
| Reverse primer | CTCGGCCTGCAATACGTTCA | 2535c |
| Helper probe 1 | CCTGGCAGGTATCGAGCACT | 1378c |
| Detection probe | ATGGAGCCTTGCGGTGCTTC | 1433c [3' DIG tail] |
| Capture probe | TTCGCCATCGAGATCACGTA | 1406c [5' biotin] |
| Helper probe 2 | TGGACAGCCAGTACGTCGGA | 1460c |
| gltA | ||
| Forward primer | CTTCACTTCAACCGCATCCT | 138 |
| Reverse primer | GGCAATCTTCATACCGTCAC | 1221c |
| Helper probe | CCATAGCACGTTCCAGAATC | 661c |
| Detection probe | GGTAGAGGCGTTCTGTTCAT | 708c [3' DIG tail] |
| Capture probe | GTGCAGGATCAGAATACGGT | 681c [5' Biotin] |
The T7-promoter sequence CTAATACGACTCACTATAGGGAGA was added in the 5'-end of each forward primer.