Figure 3

Alignment and classification of the precursor peptide MbnA. (A) A MAFFT alignment of the 20 sequenced MbnA precursors organized by family. Likely leader and core peptides are indicated on the basis of the structurally characterized Mbns and their corresponding MbnA sequences. The alignment is visualized in Jalview and residues are colored following the Taylor color scheme [109], with intensity modified by a conservation color increment of 30%. (B) Logo showing that both leader peptide and core peptide exhibit well-conserved motifs, but the leader peptide is less variant. (C) Phylogenetic tree (constructed in MEGA 5.0 as described in the Methods section) based on a ClustalOmega alignment of the 20 full MbnA. Not pictured in this tree are the three species with structurally characterized Mbns for which no genomic information exists; however, their core peptide sequences indicate that they would be grouped with Methylocystis sp. SC2 and Methylocystis rosea SV97T. Gamma distribution parameter 4.0462.