UC San Diego
Bioinformatic functional characterization of the prokaryotic FUPAs through co-localization and co- regulatory analysis : taking the FU out of the FUPAs
- Author(s): De La Mare, Russell Wade
- et al.
P-type ATPases are ubiquitous in all domains of life. Chan, et al. (2010) analyzed P-type ATPases in all the major prokaryotic phyla for which complete genome sequence data were available. The P-type ATPase superfamily consists of thirty-two recognized families, 17 of which are strictly found in prokaryotes. The first seven of these are Families 1-7, which are generally well characterized. Ten functionally uncharacterized P-type ATPase (FUPA) families were identified in as well, FUPA23 through FUPA32. Here, these families are analyzed individually rather than by phyla using the genomic context program SEED (Overbeek et al., 2005) and the co-regulation prediction program RegPredict (Novichkov PS, et al., 2010). By examining the known function of genes co-localized near those encoding FUPAs and using co-localization as a proxy for co- regulation, and finding other genes regulated by similar regulatory sequences, we are able to make highly robust predictions about the putative functions of these ATPases and functionally characterize them. In the process of doing this, unique characteristics of the proteins are illuminated and discussed in the context of phylogeny, environmental context and horizontal gene transfer and how each contributes to the functionality of these ATPases in genomes in which they are found