AMPK Methods and Protocols

redundancies due to proteins being represented both in Swiss-

Prot and TrEMBL.

10. Choose “Download” from the menu and select “Fasta (canon-
    ical)” as sequence format. Download the data also as
    tab-separated text that can be imported into a spreadsheet for
    later use. Add KO identifier (seestep 6in Subheading3.1)
    corresponding to every protein in the cross-reference file.


11. Rename the downloaded files to something meaningful, e.g.,
    AMPK-hsa.faandAMPK-hsa-xref.txt.

3.2 Compiling a Set
of Target Species

Select a representative set of target species for your analysis. If you

consider a custom search for orthologs, end with a collection of

protein sets each representing the gene set of an individual species.

eEF2K

Fig. 2Structure of the human AMPK pathway in the KEGG pathways database [13]. The AMPK is highlighted in
green, connected pathways are represented in red color

118 Arpit Jain et al.