Table 2. Mutations causing gene changes resulting in protein truncations and elongations in comparison with TPE strains.

Gene (predicted protein function)	Nucleotide change	Coordinates of change in the FB genome (CP003902.1)	Result of nucleotide change
TPFB_0012 (HP)	1 bp deletiona	12479–12487	gene shortened by 47 bp to 129 bp, gene was not annotated in the FB genome
TPFB_0040, mcp (methyl-accepting chemotaxis protein)	5 bp insertiona	49359–49373	gene shortened by 17 bp to 2433 bp
TPFB_0126b (HP)	3 bp substitution in the start codon	148982–148984	gene shortened by 42 bp to 366 bp
TPFB_0303 (TCHP)	1 bp substitution in the stop codon	319012	gene fusion of genes ortologous to TPE_0303 and TPE_0304, gene was annotated as TPFB_0303 (5076 bp)
TPFB_0347 (HMP)	2 bp insertiona	373747–373761	gene shortened by 35 bp to 711 bp
TPFB_0433, arp (Arp protein)	15 tandem repeat units, one unit was 60 bp long	462777–463676	Samoa D, CDC-2, and Gauthier, contains 12, 4, and 10 repeat units, respectively
TPFB_0461a (HP)	1 bp deletiona	493013–493022	gene elogation by 61 bp to 243 bp
TPFB_0470 (CHP)	22 tandem repeat units, one unit 24 bp long	499435–499962	Samoa D, CDC-2, and Gauthier, contains 12, 37, and 25 repeat units, respectively
TPFB_0484 (CHP)	1 bp deletiona	517701–517708	gene shortened by 309 bp to 1707 bp
TPFB_0548 (TCHP)	42 bp deletion	594092–594093	gene shortened by 42 bp to 1257 bp
TPFB_0896 (HP)	2 bp substitution leading to nonsense mutation	977039, 977041	gene shortened by 99 bp to 54 bp, gene was not annotated in the FB genome

HP- hypothetical protein, CHP – conserved hypothetical protein, TCHP – treponemal conserved hypothetical protein, HMP – hypothetical membrane protein.

^achanges in homopolymeric regions.