Additional File 1:

A conserved indel (3 aa deletion) in ClpB protein that is mainly specific for the Bacteroidales, Flavobacteriales and Flexibacteraceae species. Partial sequence alignment of the ClpB protein containing this indel region is shown. The boxed region is missing in the Bacteroidales, Flavobacteriales and Flexibacteraceae species. Dashes in the alignment show identity with the amino acid on the top line. The ClpB homologs from C. phaebacteroidetes and Methanospirillum hungatei also lack the boxed region, which could be due to LGT. The beta and gamma proteobacteria contain a larger insert in this region, which has likely occurred independently.

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Additional File 2:

Proteins that are specific for the Bacteroides Genus. All significant hits for these proteins are from the following sequenced Bacteroides species unless otherwise indicated: B. thetaiotaomicron VPI-5482, B. fragilis NCTC 9343 and YCH46.

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Additional file 3:

Proteins specific for Flavobacteria that are missing in several species. All significant hits for these proteins are also from Flavobacteriales species. However, unlike the proteins listed in Table 5, these proteins are either present in only a small number of Flavobacteria or are missing from many species.

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Additional file 4:

Chlorobi-specific proteins that are missing in some species. All significant hits for these proteins are also from Chlorobi species. However, unlike the proteins listed in Table 6, these proteins are not present in all Chlorobi species.

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