AMPK Methods and Protocols

3.4 Assessing
the Feature
Architecture Similarity
(FAS) Between
Proteins

This protocol allows analyzing and comparing feature architectures

between the identified orthologs and the corresponding seed pro-

tein. The procedure ends with a similarity measure aiding in the

conclusion whether or not an identified ortholog is likely to have

diverged in function from the seed (seeNote 9). One can manually

compare feature architectures between proteins using InterProS-

can, as explained instep 1. For an automated comparison of feature

architectures, use FAS-S, a software to assess and score the feature

architecture similarity (FAS) between two proteins. FAS scores

range from 0, i.e., two architectures share no features, to

1, when all features of the seed protein are represented in the

ortholog. The generation of FAS scores in combination with a

phyletic profiling with HaMStR_OneSeq is described insteps

2 – 5. The later FAS scoring of existing orthologous protein pairs

is outlined insteps 6– 11.

Manual comparison of feature architectures between proteins.

1. For the analysis of individual seed–ortholog pairs by eye, anno-
   tate the feature architectures with InterProScan [27]. Open the
   web interface of InterProScan, paste the protein sequence into
   the search field, and submit. You can always analyze only a
   single sequence at a time. Compare the resulting architectures
   by eye. Look out for a conspicuous absence of seed protein
   features in the ortholog and for features of the ortholog that
   are missing in the seed protein. Figures5 and 6 display the
   InterProScan annotation for PRKAA1 protein from human
   (Q13131) and of its ortholog in the fruit fly,D. melanogaster,
   (O18645), respectively. All features of the human protein are
   present in the drosophila ortholog as well. Thus, there is no

(A)

(B)

geneID H. sapiens M. musculus

PRKAA1 11

PRKAA2 11

PRKAB1 11

PRKAB2 11

PRKAG1 11

PRKAG2 11

PRKAG3 11

geneID ncbi9606 ncbi10090

PRKAA1Q13131#1.0 Q5EG47#0.9992

PRKAA2P54646#1.0 Q8BRK8#0.9984

PRKAB1Q9Y478#1.0 Q9R078#1.0

PRKAB2O43741#1.0 Q6PAM0#0.9996

PRKAG1P54619#1.0 O54950#0.9999

PRKAG2Q9UGJ0#1.0 Q91WG5#0.9996

PRKAG3Q9UGI9#1.0 Q8BGM7#0.9998

D. melanogaster S. cerevisiae A. thaliana

111

111

111

111

011

000

001

ncbi7227 ncbi559292 ncbi3702

P06782#0.9754 Q38997#0.9939

O18645#0.9760 P06782#0.9750 Q38997#0.9934

A1Z7Q8#0.9758 Q04739#0.9865 Q9SCY5#0.9950

A1Z7Q8#0.9758 P34164#0.9875 Q9SCY5#0.9944

NA P12904#0.9997 Q944A6#0.9868

NA NA NA

NA NA Q8LBB2#0.9902

M. jannaschhii C. aurantiacus

01

01

00

00

01

01

11

ncbi243232 ncbi324602

NA A9WD85#0.1306

NA A9WD85#0.1315

NA NA

NA NA

NA A9WBL7#0.9919

NA A9WHY8#0.4073

Q58799#0.9367 A9WGZ6#0.7253

O18645#0.9760

Fig. 4Different types of phylogenetic profile. (a) General format of a phylogenetic profile. The first row and first
column represent taxa and gene ids, respectively. The “1” and “0” in the cells represent the presence and
absence of orthologs, respectively. (b) Phylogenetic profile in the PhyloProfile format. The first row and first
column correspond to taxa and proteins, respectively. The cells have values in the format “OrthologId#FAS,”
where OrthologId is the protein sequence identifier, and FAS is the Feature Architecture Similarity score
between the seed and the ortholog. “NA” indicates that no ortholog was found

124 Arpit Jain et al.