Evidence for lateral gene transfer. (a) Phylogenetic tree of SPFH1 member proteins (BLOSUM matrix and neighbor joining algorithm, 1000 bootstrap replications). The ZP_01189338, YP_846427 and NP_905503 proteins, originating from bacterial species belonging to different phyla, are more closely related to each other than to SPFH1 proteins from bacterial species originating from the same phylum. (b) Phylogenetic tree of SPFH4 member proteins (BLOSUM matrix and neighbor joining algorithm, 1000 bootstrap replications). The ZP_01910769 gene from the deltaproteobacterium P. pacifica shows a closer evolutionary relationship to proteins from other phyla than to SPFH4 proteins from other deltaproteobacteria. (c) A common insertion in SPFH1 members in only distantly related species suggests lateral gene transfer. A 22 aa Insertion (aa 236–257) can be found in a few distantly related species, but in more closely related species it is missing, thereby suggesting lateral gene transfer. Compare YP_846427 of Syntrophobacter fumaroxidans (with the insertion) and YP_356078 of Pelobacter carbinolicus, both belonging to proteobacteria; compare ZP_01189338 (with insertion) of Halothermothrix orenii and NP_844475 of Bacillus anthracis, which belong to firmicutes; compare NP_905503 (with insertion) of Porphyromonas gingivalis and ZP_00593072 from Prosthecochloris aestuarii which belong to bacteroidetes. (d) Codon usage of the NP_905503 gene (1) compared with codon usage of total coding sequences in P. gingivalis (2), for the YP_846427 gene (3) compared with total coding sequences of P. fumaroxidans (4), of the ZP_01189338 gene (5) compared with total coding sequences of H. orenii (6) and of the YP_144313-15 operon (7) compared with T. thermophilus total coding sequences (8). Synonymous codons are shown to the right of each amino acid and color-coded to match the percent usage indicated by the bars.