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The six clones pTB112, pTB324, pTBs12, pCd122, pCd14 and pCdl3 cover thetox locus ofClostridium difficile VPI 10463. This region of 19 kb of chromosomal DNA contains four open reading frames including the completetoxB andtoxA genes. The two toxins show 63% amino acid (aa) homology, a relatedness that had been predicted by the cross-reactivity of some monoclonal antibodies (mAb) but that is in contrast to the toxin specificity of polyclonal antisera. A special feature of ToxA and ToxB is their repetitive C-termini. We define herein 19 individual CROPS (combinedrepetitiveoligopeptides of 20–50 as length) in the ToxB C-terminus, which are separable into five homologous groups. Comparison of the as sequences of the N-terminal two-thirds of ToxA and ToxB revealed three marked structures, a cluster of 172 hydrophobic, highly conserved as in the centre of both toxins, a sequence of 120 residues with an accumulation of highly conserved arginine, cysteine, histidine, methionine, and tryptophan residues, and a stretch of 248 less conserved aa. The probable function of these domains is discussed. Structural and functional homologies of ToxA and ToxB indicate that both genes have a common ancestor and may have evolved by gene duplication, with subsequent recombination and mutation, as has been reported for streptococcal glucosyltransferases (Gtf).