NHE1-9, Nhx1 and NhaA belong to the CPA superfamily15 and are classified in the Monovalent Cation:Proton Antiporter-1 (CPA1) Family (2.A.36) on TCDB6 database55. The only crystal structure available for this superfamily is the bacterial ortholog NhaA35. NHE9, Nhx1 and NHE1 share a sequence identity of only 14, 15 % and 10% with NhaA, respectively. These low sequence identities limit the alignment of sequences using standard methods. To confirm that we were using the template with the correct fold we used the tools available on the “Transporter classification database (TCDB) (http://www.tcdb.org/)” and “Protein Data Bank (PDB) (http://www.rcsb.org/pdb/home/home.do)”. Searching the PDB starting with the NHE9 query, the first hit is the NhaA structure (1zcd). The second hit is the bile acid transporter ASBT (3zux), which shares a similar fold but has only 10 transmembranes. The next hits are the transmembrane XI of the NHE1 isoform56. The other hits include NHE1 transmembrane XI, a putative YscO homologue (3k29; in the C-terminal region), Stathmin 4 (1sao; in the C-terminal region), and Aquaporin-4 (1ivz; 340 residues). The last hit (number 10) is Histone deacetylase 4 (2h8n; in the C-terminal region).
