Bioinformatic characterization of the copper and heavy metal families of P-type ATPases

P-type ATPases are classified as the 3.A.3 Superfamily in the Transport Classification Database (TCDB) and are an important group of protein pumps involved in the translocation of specific ions or phospholipids across biological membranes. The 3.A.3. Superfamily presently consists of thirty-four families of P-type ATPases, only ten of which are functionally characterized. Methodical analyses of sequences from each of these families are required to elucidate the mechanism by which they transport their substrates and to identify their distinguishing functional characteristics. A phylogenetic tree was constructed to confirm that sequences representing the 3.A.3. Superfamily in TCDB reflected their family assignments, and that the sequence characteristics of each "sub-superfamily" cluster within this tree were examined. The Copper and Heavy Metal P-type ATPase families were subsequently selected for more in- depth analyses. Protein sequences representing these two families were collected using NCBI psi-BLAST, multiply aligned, and analyzed using protein and 16S rRNA phylogenetic trees. The sequence similarities within each family, with regard to sequence length and conservation of specific amino acid motifs, were examined and compared. Additionally, the secondary structure patterns, regions of amphipathicity and hydrophobicity, and predicted numbers and locations of transmembrane segments (TMSs) for these sequences were analyzed. Most sequences from both families showed conservation of nine well-described motifs and exhibited a consistent pattern of eight TMSs. Sequence homology analyses revealed that while most sequences clustered with others from their genus or phylogenetic group, some sequences were so divergent from their neighbors that they could indicate instances of horizontal gene transfe