AMPK Methods and Protocols

Species

Proteins

PRKAA1

PRKAA2

PRKAB1

PRKAB2

PRKAG1

PRKAG2

PRKAG3

1001_Chordata1002_Cnidaria

1003_Platyhelminthes

1004_Nematoda1005_Arthropoda

1006_Basidiomycota1007_Ascomycota1008_Opisthokonta1009_Amoebozoa

1010_Fornicata1011_Euglenozoa1012_Apicomplexa

1013_Bacillariophyta1014_Streptophyta1015_Parabasalia1016_Euryarchaeota1017_Crenarchaeota

1018_Candidatus Korarchaeota

1019_Proteobacteria1020_Fusobacteria1021_Nitrospirae1022_Dictyoglomi

1023_Aquificae

1024_Thermotogae1025_Spirochaetes1026_Planctomycetes1027_Chlamydiae1028_Bacteroidetes1029_Cyanobacteria1030_Firmicutes

1031_Deinococcus−Thermus

1032_Chloroflexi1033_Actinobacteria

0.250.50

0.751.00

FAS

presSpec0.00

0.250.50

0.751.00

0

Traceability

(A) (B)

(C)

0

0.97

0 0 0

0.03

cast_S−rich

pfam_AdenylateSensor

seg_lowcomplexityregions

smart_RIO

PRKAA1:HUMAN - 0.976

PRKAA1:DROME - 0.976

0.84

0 000

0.03

0

0.01

0

0

0.09

0.01

0

0

pfam_AdenylateSensor

seg_lowcomplexityregions

smart_RIO

cast_P−rich

pfam_Kinase−like

pfam_Pkinase

pfam_Pkinase_Tyr

pfam_RIO1

smart_KIND

smart_S_TKc

smart_TyrKc

0 200 400 600

(^0200400600)
Fig. 7Visualization of phylogenetic profiles using PhyloProfile. (a) Phylogenetic profile of the human AMPK
pathway. The color code represents the FAS score. (b) Customized phylogenetic profile for seven AMPK
proteins: PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKAG1, PRKAG2, and PRKAG3. Species are summarized on
the phylum level. The size of the dots indicates the fraction of species in a phylum with an ortholog present. (c)
Domain architecture comparison between human PRKAA1 (above) and its ortholog in yeast (below). Note that
the FAS-S algorithm ignores the accumulation of redundant features annotated in the N-terminal half of the
yeast ortholog. All main features of the human protein are observed also in the yeast sequence, and hence we
have no reason to assume functional divergence of the two proteins
Tracing AMPK Evolution 129