On 2017 Jul 11, Daniel Haft commented:

Readers may wish to note that the passenger domain of this autotransporter has multiple copies of repeat that averages about 88 residues in length, with consensus sequence GDNTYAGGTEVEAGTLRVSRDANLGAAAGAVTLDGGALAATASFASARALTLKAAGALDVAAGTTLDWRGAVSGAGKLVKEGAGTLVL. The BatB orthologs discussed in this paper have 17 repeats in Bordetella pertussis and B. bronchiseptica, and 11 repeats in B. parapertussis. The deletion of 531 amino acids in B. parapertussis maps to this repeat region. Additional batB gene translations from Bordetella isolates obtained since this paper show additional examples of changes in the numbers of repeats. Since individual repeats are quite different from each other, these changing repeat copy numbers very likely represent natural variation, not sequencing and assembly errors. Therefore, the shorter form seen in B. parapertussis should not be viewed as non-functional simply because it shows a large deletion relative to B. pertussis.

On 2017 Jul 11, Daniel Haft commented:

Readers may wish to note that the passenger domain of this autotransporter has multiple copies of repeat that averages about 88 residues in length, with consensus sequence GDNTYAGGTEVEAGTLRVSRDANLGAAAGAVTLDGGALAATASFASARALTLKAAGALDVAAGTTLDWRGAVSGAGKLVKEGAGTLVL. The BatB orthologs discussed in this paper have 17 repeats in Bordetella pertussis and B. bronchiseptica, and 11 repeats in B. parapertussis. The deletion of 531 amino acids in B. parapertussis maps to this repeat region. Additional batB gene translations from Bordetella isolates obtained since this paper show additional examples of changes in the numbers of repeats. Since individual repeats are quite different from each other, these changing repeat copy numbers very likely represent natural variation, not sequencing and assembly errors. Therefore, the shorter form seen in B. parapertussis should not be viewed as non-functional simply because it shows a large deletion relative to B. pertussis.