TABLE 2.
Primer sequences and characteristics of housekeeping gene loci included in the S. mutans MLST scheme
| Locus | Gene locus tag and putative function of gene products | Primer names | Primer sequences (5′ to 3′) | Size of sequence fragment (bp) | No. of alleles identified | No. (%) of polymorphic nucleotides | dN/dS | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|
| tkt | Smu.291, transketolase | tktF | ACC CGG GTG TTG TCA TGG GCG CTG C | |||||
| tktR | CAT AGG ATG ACG CTT CGC CAG AAA C | 432 | 14 | 16 (3.70) | 0.1032 | AB281702-AB281802 | ||
| glnA | Smu.364, glutamine | glnA-F | CCT TGG GGA GAT GAA AAC GGA GCC G | |||||
| synthetase | glnA-R | TGG CCA TAA AGG TTG CAT ACA AAC C | 462 | 16 | 15 (3.24) | 0.0628 | AB281803-AB281903 | |
| gltA | Smu.365, glutamate | gltA-F | TGC CTT AAC GAT GTT AGA GAG AAT G | |||||
| synthase | gltA-R | AAA GAC TAT CTT CAA AAG CAC ACC C | 387 | 23 | 21 (5.43) | 0.2082 | AB281904-AB282004 | |
| glk | Smu.542, glucose | glk-F | GAC AAG TTC AGG AGA AAT GGG CTA T | |||||
| kinase | glk-R | CAG CAA CTC CAT GAA TAA GAT TGC C | 402 | 19 | 16 (3.98) | 0.6333 | AB282005-AB282105 | |
| aroE | Smu.778, Shikimate | aroE-F | GAT GAA GTA ACG AAA GCA GCA GAT T | |||||
| 5-dehydrogenase | aroE-R | TGC CAT CCA TAC CAA CAT TGG TCG C | 396 | 21 | 19 (4.80) | 0.4467 | AB282207-AB282307 | |
| gyrA | Smu.1114, DNA gyrase | gyrA-F | TAC AGG TGA TGT CAT GGG TAA ATA C | |||||
| subunit A | gyrA-R | CCG GGT AGT ACT TCC ATT AGG TCA C | 432 | 17 | 17 (3.94) | 0.1520 | AB282106-AB282206 | |
| murI | Smu.1718, glutamate | murI-F | TCC GGA GTG GGC GGT TTA ACG GTC G | |||||
| racemase | murI-R | TCA ACA ATA GGA ACA AAT TTG GGG C | 423 | 15 | 17 (4.02) | 0.0544 | AB282308-AB282408 | |
| lepC | Smu.1874, signal | lepC-F | CCG CGT CTC TTT ATC TGG TTT CTT G | |||||
| peptidase I | lepC-R | GAC AAT GCG ATC ATC ACC TAA AAG C | 417 | 23 | 19 (4.56) | 0.1305 | AB282409-AB282509 |