TABLE 3.
Constructed primer pairs used in this study
| Group | Target gene (synonym) | PCR product size (bp) | Annealing temp (°C) | Primer | Sequence | Product |
|---|---|---|---|---|---|---|
| 1 | STM3098 | 423 | 65 | STM3098-f2 | 5′-TTTGGCGGCGCAGGCGATTC | Putative transcriptional regulator |
| STM3098-r2 | 5′-GCCTCCGCCTCATCAATCCG | |||||
| STM4444 | 253 | 65 | STM4444-f | 5′-ATGCCGACTGGTCGTTCCCG | Putative inner membrane protein | |
| STM4444-r | 5′-CCCACGCCGGTCTGAATTGC | |||||
| 2 | STM0349 | 249 | 65 | STM0349-f | 5′-TCGTCGGCTTGGCTTTAACC | Putative outer membrane lipoprotein |
| STM0349-r | 5′-CTGCACGCTGGGTTAACAGG | |||||
| STM4030 | 310 | 65 | STM4030-f | 5′-AAACCGTCCCACTGATGGGG | Putative cytoplasmic protein | |
| STM4031-r | 5′-CGTTAGTGCTCTGCGGCCAT | |||||
| 3 | STM1550 | 187 | 67 | STM1550-f | 5′-AGCTAAGGGAACGGCTTGAA | Putative cytoplasmic protein |
| STM1550-r | 5′-CGTGTCATTTTGTAGACGGC | |||||
| STM2235 | 177 | 65 | STM2235-f | 5′-TGCAGTCAGTGGCAATAACG | Putative phage protein | |
| STM2235-r | 5′-CGTCACCTTTAGCCATCCCA | |||||
| STM2630 | 115 | 65 | STM2630-f | 5′-CTGCCGCAAATCCATTGATG | Hypothetical protein | |
| STM2630-r | 5′-GTATTCAGCGCACTGCCTGG | |||||
| STM2744 | 141 | 65 | STM2744-f | 5′-CCGAAAGCGGCAACGTGCGT | Putative cytoplasmic protein | |
| STM2744-r | 5′-CCGCAGCATCGAAGACCACC | |||||
| STM2752 | 203 | 65 | STM2752-f | 5′-TTATTCCTCCCGGTCCCGGC | Putative glucitol-specific PTS enzyme III | |
| STM2752-r | 5′-CCCGGCGCAGTTAATCACCA | |||||
| STM2755 | 187 | 65 | STM2755-f | 5′-AGCTGCTTTTCGACGCCGGG | Putative hexulose 6 phosphate synthase | |
| STM2755-r | 5′-ACCGCCAGCATATCTGCCCC | |||||
| STM4203 | 316 | 65 | STM4203-f | 5′-CTGCCTTGCAACGTCCTGAA | Putative phage baseplate protein | |
| STM4203-r | 5′-CGCCATAACACCTCCGTTGA | |||||
| STM4214 | 109 | 65 | STM4214-f | 5′-ACGCTCGCCGACGGTCAGGA | Putative cytoplasmic protein | |
| STM4214-r | 5′-CTGGCACCAGGTGACGGCGG | |||||
| STM4497 | 310 | 63 | STM4497-f | 5′-AACAACGGCTCCGGTAATGA | Putative cytoplasmic protein | |
| STM4497-r3 | 5′-TGACAAACTCTTGATTCTGA | |||||
| STM4571 | 154 | 65 | STM4571-f | 5′-TTTGTGCAGGCCTCAGCGGG | Putative outer membrane protein | |
| STM4571-r | 5′-GGGCACTGTCATTGGGAGCA | |||||
| 4 | STM2453 | 270 | 65 | STM2453-f | 5′-TTGTATGCCCTGCGTCCAGG | Putative cytoplasmic protein |
| STM2453-r | 5′-GCTTCCTCCTGCCATCCGGA | |||||
| STM2624 | 284 | 65 | STM2624-f | 5′-CTGGTGAAAGAGCAGGGGCG | Hypothetical protein | |
| STM2624-r | 5′-GCTCCCCCCTTGTTGATGCT | |||||
| 5 | STM1269 | 425 | 65 | STM1269-f | 5′-GTGCAGCACCACTTTTGCCG | Putative chorismate mutase |
| STM1269-r | 5′-GCGCTCTCAGCCACACCATA | |||||
| STM1277 | 289 | 65 | STM1277-f | 5′-AAGCGCGTCTATTTCCCGGC | Putative cytoplasmic protein | |
| STM1277-r | 5′-GGCGAGTATCTTTAGCGGCG | |||||
| 6 | STM0538 | 288 | 65 | STM0538-f | 5′-TCTCTTCCACAGTCCCCGCT | Putative outer membrane protein |
| STM0538-r | 5′-CTGTCGCCGCTGTTTAGCCC | |||||
| STM3532 | 233 | 65 | STM3532-f | 5′-TCCGCCAGTTCCGACCATTG | Putative dihydrodipicolinate synthetase | |
| STM3532-r | 5′-CCTGCGTGCTGGTGCTGCTA | |||||
| 7 | STM4509 | 312 | 65 | STM4509-f | 5′-TGGCGTTCCGTCCTTGTCAG | Putative cytoplasmic protein |
| STM4509-r | 5′-TTGCGCCCTTATCACGACGG | |||||
| 8 | STM0305 | 155 | 65 | STM0305-f | 5′-CGGAAACAGGACGGGGCTGT | Putative cytoplasmic protein |
| STM0305-r | 5′-CCGAAGGCGCAATGGAGGAT | |||||
| STM1408 | 187 | 65 | STM1408-f | 5′-TCCTCTGCAGAACCGAGCCA | Type III secretion system apparatus protein | |
| STM1408-r | 5′-TAAGCGCTTGCGATGCTGCG | |||||
| STM1859 | 115 | 65 | STM1859-f | 5′-AACACGATGCCATTTTCAAT | Putative cytoplasmic protein | |
| STM1859-r | 5′-TTGAGGTCAGTGTGCAATTC | |||||
| STM2056 | 342 | 65 | STM2056-f | 5′-TGATGTTTATCGGCCCCAGC | Propanediol utilization protein | |
| STM2056-r | 5′-CCAGCCTGCGTAAGCCACTC | |||||
| STM3690 | 268 | 65 | STM3690-f | 5′-GAAGTCGTTGGCCGCGTTGA | Putative inner membrane lipoprotein | |
| STM3690-r | 5′-GGAGTTGTTTCCAGCGAGGC | |||||
| STM4057 | 137 | 65 | STM4057-f | 5′-GGTGGCCTCGATGATTCCCG | Putative inner membrane protein | |
| STM4057-r | 5′-CCCACTTGTAGCGAGCGCCG | |||||
| STM4071 | 167 | 65 | STM4071-f | 5′-AAGCGGTGAAGTGTGCCTGT | Putative mannose-6-phosphate isomerase | |
| STM4071-r | 5′-CGGGGTGGCTGTCATTTTCC | |||||
| STM4317 | 220 | 65 | STM4317-f | 5′-GCGAAACCCTGAACCTGCGT | Hypothetical protein | |
| STM4317-r | 5′-CGCAGTGCGGCATTAGGTGA | |||||
| STM4457 | 215 | 65 | STM4457-f | 5′-AGCAACAGCACGCTCCGTCG | Putative transposase | |
| STM4457-r | 5′-GATATGCGACGAAAGCGGCG | |||||
| 9 | STM0339 | 232 | 65 | STM0339-f | 5′-GCCCTACCCGCCACAGCATC | Putative fimbrial chaperone |
| STM0339-r | 5′-CCTGGCCTGCTTTGGGTTGA | |||||
| 10 | STM1006 | 165 | 65 | STM1006-f | 5′-TCTGATTGCGGTTACCGGGC | Excisionase |
| STM1006-r | 5′-TGCGCCTCGATCCACTGATC | |||||
| 11 | STM3752 | 165 | 65 | STM3752-f | 5′-CGGCTTGGCGTATACAGCGA | Putative cytoplasmic protein |
| STM3752-r | 5′-GCCTCCCTCCAGATACACGG | |||||
| 12 | STM0287 | 328 | 65 | STM0287-f | 5′-CGTATTTGCCTGGGGCGGAA | Putative periplasmic protein |
| STM0287-r | 5′-CGCCAGCTTCTGATCCCGTA | |||||
| 13 | STM2434 | 103 | 65 | STM2434-f | 5′-AGATATCTGCGTGGCGCGAG | Putative cytoplasmic protein |
| STM2434-r | 5′-ATCCGGGCCACTCTCCAGCA | |||||
| 14 | STM4596 | 573 | 65 | STM4596-f | 5′-ATGAAGCAGTTAAACGGCGG | Putative inner membrane protein |
| STM4596-r | 5′-GCTGCGTGAAAGCCCGGTTC | |||||
| 15 | STM2955S | 186 | 65 | STM2955-f | 5′-CTTGGCGATGAACTGCGCGA | Putative transcriptional regulator |
| STM2955-r | 5′-CTTTTCCCAGGCCTGCGGCT | |||||
| 16 | STM0409 | 170 | 65 | STM0409-f | 5′-TCGGGAAACCATGGATGGGG | Hypothetical protein |
| STM0409-r | 5′-CACCGGCAAGGACGACACGT |