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. Author manuscript; available in PMC: 2014 Sep 18.
Published in final edited form as: Annu Rev Biochem. 2014 Mar 3;83:753–777. doi: 10.1146/annurev-biochem-070611-102400

Figure 2.

Figure 2

Phylogenetic distribution of small proteins. Unrooted prokaryotic phylogenetic tree based on 16S rRNA sequences, adapted from Nelson et al. (106). Center: selected major phylogenetic groupings are colored and selected organisms are indicated. Phylogenetic distribution of small proteins discussed in this review are grouped according to biological function and highlighted in red on individual trees shown at lower magnification. Homologs were identified by a PSI_BLAST search of 2262 completely sequenced genomes (as of February 2013). A table summarizing the presence of absence of particular small proteins is given as Supplemental Table 1. This analysis illustrated the disparate nature of small protein annotation; for example, the pmrR gene is annotated in only six out of the 95 genomes in which homologs were found. The alignments of annotated small proteins generated by MUSCLE are given in Supplemental Table 2 and are available in FASTA format at ftp://ftp.ncbi.nih.gov/pub/wolf/_suppl/small.