MLST Pasteur Web Site






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Primers used for MLST of Streptococcus thermophilus

- Genes

The Streptococcus thermophilus MLST scheme uses internal fragments of the following six housekeeping genes:

ddlA (D-alanine--D-alanine ligase)

glcK (glucose kinase)

proA (gamma-glutamyl phosphate reductase)

ptsI (phosphoenolpyruvate-protein phosphotransferase)

serB (phosphoserine phosphatase)

tkt (transketolase)

- Primers for PCR amplification

ddlA : F : ddlA up : TCAAGTGTGGCTATGGA

ddlA : R : ddlA down : GTAGATGGCTCCATCCTC

glcK : F : glcKup : TGGGCAGAAACTCAAGA

glcK: R : glcKdown : AACACCACCACCGATAAC

proA : F : proA up : CCCGTCTCATCCAAACTGTG

proA : R : proA down : TGGTTGAAGTTAGGGCCTCA

ptsI : F : ptsI up : ACGTACTAGTCACTCTGCAA

ptsI : R : ptsI down : CACGAAGCAAGGCACGTAAT

serB : F : serB up : GGTCCAAGAAGAAGTAATTGA

serB : R : serB down : GACCTTATACAAATCTGGTT

tkt : F : tkt up: GCAGCACACCAATGGGTTACAC

tkt: R : tkt down : GGAGCACCATGACCAATG

- Sequencing primers

The same primers as for PCR are used.

- PCR conditions

PCR amplification is performed at an annealing temperatures of 54°C for all genes.

- Allele templates

ddlA (450 bp)

CTTGAAGTTGCTGGAGTGCCACAGGTTGCCTACACAGGCTACATCGAGGGTGAAGATTTGGAAGCAGCAGTAGCAG AGACACTTGAAAAATTGACCTTCCCAGTTTTTGTCAAACCAGCCAACATGGGGTCATCTGTTGGGATTTCTAAAGC TGAAAATGAATCAGAGCTTCGTTCAGCGATTGATCTTGCTCTCAAATATGATAGCCGTATCTTGATTGAGCAAGGT GTAGTTGCTCGTGAAATCGAAGTTGGTATCCTTGGAAATACGACTGTCAAAACGACTGATCCGGGTGAAGTGGTCA AAGACGTGGCTTTCTATGATTACCAAGCCAAGTACATTGACAATAAGATTACCATGGATATTCCAGCTCGCGTGCC TGTCGAAGTCATGACGCAAATGCGTGCCTATGCGGCCAAGGCCTTTCGTGCTCTAGGGGGTTGCGGTCTT

glcK (450 bp)

CTTGGTATTCCATTCGCTATTGATAATGATGCTAATGTGGCTGCACTGGGTGAACGTTGGGTTGGTGCTGGTGCTA ACAATCGGAATGTTGTCTTTATAACATTGGGTACAGGTGTTGGTGGCGGTGTTATCGCTGATGGTAACTTAATTCA TGGTGTTGCCGGTGCTGGTGGGGAAATTGGTCACATTATTGTTGAACCTGACACAGGATTTGAGTGTACTTGCGGA AACAAGGGGTGTCTGGAAACTGTAGCTTCAGCAACAGGTATTGTACGTGTAGCACATCATTTGGCAGAAAAATACG AAGGAAACTCTTCTATTAAAGCTGCTGTAGACAATGGTGAGTTTGTGACAAGTAAAGATATTATCGTAGCTGCTAC TGAAGGTGATAAGTTTGCTGACATCATTGTTGATAAAGTCTCTAAATACCTCGGACTTGCAACAGCAAAC

proA (519 bp)

CCAGTCATCGAAACGGGTGTTGGTAACTGTCATATTTATGTGGATAAATATGCTAACTTAGATATGGCGACACAGA TTGTCATCAATGCCAAGACCCAACGACCAAGTGTGTGTAATGCTGCAGAATCTCTCGTTGTTCATGCTGATATTGT AGAAGAATTCTTGCCTAACTTGGAAAAAGCTATTTCAAAAATTCAGTCTGTTGAGTTCCGCGCGGATGAAAGGGCT TTGAAACTTATGGAAAAAGCTGTACCCGCTTTACCAGAGGATTTTGCGACAGAGTTTCTTGACTACATTATGTCTG TTAAAGTAGTAGACAGCCTTGATGAGGCGATTAATTGGATTAATACTTACACGACATCACATTCAGAAGCTATCGT GACTCAGGATATCAGTCGTGCTGAGCAATTCCAAGACGATGTTGACGCTGCAGCTGTCTATGTCAATGCCTCGACT CGTTTCACAGACGGTTTCGTCTTTGGACTGGGTGCTGAAATCGGAATCTCAACCCAAAAAATG

ptsI (501 bp)

GTCCTTGGAATAAACAACATAACTGAACTTGTTAAAGATGGTGACATTTTAGCGGTTTCAGGTATTACCGGTGAAG TTGTTATTAATCCAACTGAAGAACAAATTGCTGAGTTTAAAGCAGCTGGTGAAGCTTACGCCAAACAAAAGGCAGA ATGGGCTCAACTTAAAGATGCTCCAACAGTTACTGCTGATGGAAAACACTTCGAGTTAGCAGCAAATATCGGTACA CCTAAAGACGTTGAAGGTGTTAACGATAATGGTGCAGAAGCAGTTGGTCTTTATCGTACAGAATTCTTGTATATGG ATTCTCAAGATTTCCCAACCGAAGAAGACCAATATGAAGCATACAAAGCAGTTCTTGAAGGTATGAATGGTAAACC TGTTGTTGTTCGTACAATGGATATCGGTGGGGATAAAGAACTTCCTTACTTTGACCTTCCTAAAGAAATGAATCCA TTCTTGGGTTACCGTGCATTACGTATTTCTATCTCTGAAACTGGT

serB (498 bp)

GAGGCTGGTGTTGGTCGAGAGGTCGCTGAAATCACAGAGCGGGCCATGCGTGGAGAATTAGATTTCAGACAGGCTT TGAATGAGCGTGTGGCAACCCTTAAGGGATTGCCTGACAGTATATTTGAGAAGGTCTATGCCCGCATTCATTTCAA CAAGGGAGCCAAGGAACTTGTGGATGAACTCCACTCACGTGGCTTCAAGGTAGGTTTAGTTTCTGGTGGTTTCCAT GAGACAGTTGATAGACTGGCAAAAGAGGCAGGTATTGATTATGTGAAGGCCAATCACCTTGAGGTGATCGATGGTT TCTTAACTGGAAAGGTTTATGGTGAGATTGTTACCAAAGATGTCAAGGTAGCTAAGCTTAAAGATTGGGCAGCGGA AAATGGACTTAAGCTCTCTCAAACCATTGCTATGGGTGATGGAGCCAATGATTTGCCTATGATTAAGACAGCGGGT ATAGGCATCGCCTTTTGTGCCAAACCAATTGTCCGTGTACAA

tkt (525 bp)

CGTTTTGTTTTGTCAGCAGGTCATGGTTCAATGCTTCTTTATGCGCTCCTTCATTTGTCAGGATTTAAAGATTTGA GCATTGAAGAGCTTAAACAATTCCGTCAATGGGGTTCTAAGACACCTGGTCACCCAGAATTTGGCCATACAGTTGG TGTAGATGCTACGTCAGGTCCACTTGGGCAAGGTATTGCTATGGCTGTCGGTATGGCACAAGCTGAACGTTTCTTG GCTTCTCGATACAACAAGGAAGGCTTCCCAATCTTTGACCATTATACTTATGTTATTGCGGGAGATGGTTGCTTTA TGGAAGGCGTTTCGGCCGAAGCATCATCTTACGCTGGTCTTCAAAAATTGGATAAATTGATTGTCTTGTACGATTC AAATGATATCAATCTTGACGGTGAAACTAAAGATTCATTTACTGAAGATGTACGTGCACGTTATGAAGCTTATGGT TGGAACACTGAATTTGTTCAAGATGGAACAGATATTGAAGCTATCAACGCTGCTATTGAAAGTGCAAAA



Databases are maintained by Sylvain Brisse using software developed by Keith Jolley at Oxford (Jolley et al. 2004, BMC Bioinformatics, 5:86). Web managers : Ghislaine GUIGON and Jean-michel THIBERGE This site is hosted by the technological platform Genotyping of Pathogens and Public Health* of Institut Pasteur.*