Figure 4

Protein family curation with ITEP. (A) A portion of the multiple alignment for the uncalled ribosomal protein L20 homologs in Acetobacterium woodii and C . perfringens str. CPE F4969, along with selected representatives of this protein from other Clostridia. Blue amino acids were conserved in more than 50% of the aligned proteins and pink amino acids are similar to the conserved acids. The figure in part (A) was generated by importing a multiple alignment generated by an ITEP script into the STRAP aligner [46]. (B) Gene neighborhoods for the proteins from part (A) attached to the maximum-likelihood phylogeny of the same proteins. Same-colored arrows indicate that the genes belonged to the same family according to MCL with the same parameters used to construct Figure 2. The visualization was done with an ITEP script.