UC San Diego

The Major Facilitator Superfamily (MFS) [1] is currently the largest characterized superfamily of transmembrane secondary transport proteins [2]. Its diverse members are found in all organisms in the biosphere and function by uniport, symport, and/or antiport mechanisms. In 2012 we described a total of 74 recognized families, classified phylogenetically within the MFS, all of which included only transport proteins [3]. In this study, we assign several previously uncharacterized transport protein families in the Transporter Classification Database (TCDB; http://www.tcdb.org) to the MFS using established statistical methodologies. In addition, relationships at the superfamily level between the Major Facilitator Superfamily (MFS) and the (LysE) Superfamily have been discovered. Specifically, for the MFS having a common origin with the Resistance to Homoserine/Threonine Family (RhtB; TC# 2.A.76), Tellurium Ion Resistance Family (TerC; TC# 2.A.109), and (17) Nickel/cobalt Transporter (NicO; TC# 2.A.113) is presented. Global alignments and hydropathy plots of transport proteins were generated to assist in determining homology. The use of several sequence analysis programs to search for internal repeats, combined with existing protein structural data, provide strong evidence that the ubiquitous 12 transmembrane segment (TMS) topology arose from a 6 TMS gene duplication which in turn, arose from a 3 TMS duplication. Furthermore analysis of PFAM domains, 3D structures, provided further evidence for homology. Negative control studies were conducted between members of TCDB that are currently not known to be members of the MFS to ensure statistical significance. Positive control studies were conducted between members currently within the MFS.