Figure 1

The number of LacI-family TF homologs and the presence of Lactobacillus plantarum orthologs in different Firmicutes. The organisms are organized on basis of their phylogeny (left; inferred from phosphoglycerate kinase amino acid sequence data [98]) and the TFs on basis of the NJ-tree of the L. plantarum LacI-family TFs (top). The presence of an ortholog to the L. plantarum proteins is indicated by open (different cluster in the NJ-tree) and closed circles (same cluster in the NJ-tree). The members of the various L. plantarum GOOFEs are colored. Some orthologs have been experimentally characterized and are indicated by '+'. remark: Although the PFAM HMM that is used to identify the LacI-domain represents only a small part of the DNA-binding domain, in most instances there was complete correspondence between the number of LacI-family TFs identified by us and the number listed by PFAM [96]. However, there were a few exceptions and in these cases the number given by PFAM appeared erroneous [see Additional file 1]. In some cases the PFAM database was just incomplete (e.g. Pediococcus pentosaceus and Leuconostoc mesenteroides). In other cases sequences were counted twice as a result of double Uniprot entries (e.g. for CcpA in L. plantarum). Other proteins were missing in the PFAM database because of mistakes in the ORF definition.