Proteins with phylogenetic profiles in the neighborhood of ribosomal protein RL7 (A), flagellar structural protein FlgL (B), and histidine biosynthetic protein His5 (C). In each case, we first found all proteins with profiles identical to our query proteins; the proteins we found are shown in the double boxes. We then found all the proteins with profiles that differed from our query proteins by one bit; these are shown in the single boxes. Proteins in bold participate in the same complex or pathway as the query protein, and proteins in italics participate in a different but related complex or pathway. Proteins with identical profiles are shown within the same box. Single lines between boxes represent a one-bit difference between the two profiles. All neighboring proteins whose profiles differ by one bit from the query protein are shown. Homologous proteins are connected by a dashed line or are indented. Each protein is labeled by a four-digit E. coli gene number, a SwissProt gene name, and a brief description. Note that proteins within a box or in boxes connected by a line have similar functions. Hypothetical proteins (i.e., those of unknown function) are prime candidates for functional and structural studies. Proteins in the double boxes in A, B, and C have 11, 6, and 10 ones, respectively, in their phylogenetic profiles, of a possible 16 for the 17 genomes presently sequenced.