TABLE 1

List of primers used in this study and sequence information

Gene(s)Primer namePrimer sequence (5′ to 3′)Position(s)aTrimmed amino acid sequence (positions)bNo. (%) of variable nucleotide sites/total no. of nucleotide sitsfNo. (%) of variable amino acid sites/total no. of amino acid sitesf
pbp1apbp1a-fACIACDGGDATGGAHGTHTA877–896318–577371/780 (48)98/263(37%)
pbp1a-rGTCCADACRGCCATWGMATA1790–1771
pbp2bpbp2b-fAATGAYCGHGTBGGDACYTC793–812440–643294/612 (48)79/204 (39)
pbp2b-rTTGATRATRTCRCGHGCAAT2027–2008
pbp2xpbp2x-fAAGTAYATGACIGCDACCTT862–881308–554320/741 (43)79/247 (32)
pbp2x-rTGVAGRTTRAGRGADTCTTT1865–1846
murM and murNmurMN-fCAYGARTGGTAYTAYTGGGAA694–714c
murMN-rTGAATRTARCAWCCAGGRCT62–43d
Ortholog of murMmurM_uo5-fTTGCARAGTAGTGATTGGKCCA76–97e
murM_uo5-rTCCTTTATTYYTTGCAGTTCGGA556–534e
  • a Nucleotide positions according to the S. pneumoniae R6 sequence.

  • b Amino acid positions in S. pneumoniae R6. Active sites range from residue 337 to residue 549 (pbp2x), 386 to 617 (pbp2b), and 370 to 557 (pbp1a).

  • c Nucleotide position in the flanking SP_0614 gene in S. pneumoniae R6 of the mugsy cluster of murM and murN.

  • d Nucleotide position in the flanking SP_0618 gene in S. pneumoniae R6 of the mugsy cluster of murM and murN.

  • e Nucleotide position in the ortholog of the murM gene in S. oralis uo5.

  • f Numbers of all variable sites for all strains included in the sequence analysis.