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Computational Molecular Biology 2014, Vol. 4, No. 7, 1-17
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activity (21.1%), peptidase (15.7%), oxidoreducatases
(14%), and some other enzymatic activities. Fungal
secreted proteins are involved in more than 60
different biological processes. The main biological
processes include catabolic process (24.6%),
carbohydrate (22.0%) or lipid (4.0%) metabolic
process, cell wall organization or biogenesis (6.4%),
response to stress, small molecule and nitrogen
metabolic process, etc. It should be noted that GO
classification was only an estimate of the distributions
of each category as ~54% of the predicted secreted
proteins do not have GO annotation information.
Table 3 Gene Ontology (GO) classification of fungal secreted proteins
GO ID
Count
%
GO description
Molecular function
GO:0016798
16132
30.9
hydrolase activity, acting on glycosyl bonds
GO:0043167
11011
21.1
ion binding
GO:0008233
8182
15.7
peptidase activity
GO:0016491
7305
14.0
oxidoreductase activity
GO:0016829
1710
3.3
lyase activity
GO:0016791
1439
2.8
phosphatase activity
GO:0016810
1242
2.4
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016853
1010
1.9
isomerase activity
Others
4136
7.9
including 32 other GO categories
Total
52167
Biological process
GO:0009056
21356
24.6
catabolic process
GO:0005975
19039
22.0
carbohydrate metabolic process
GO:0071554
5584
6.4
cell wall organization or biogenesis
GO:0009058
3612
4.2
biosynthetic process
GO:0006629
3463
4.0
lipid metabolic process
GO:0006950
3405
3.9
response to stress
GO:0044281
3356
3.9
small molecule metabolic process
GO:0034641
3076
3.5
cellular nitrogen compound metabolic process
Others
23845
27.5
including 60 other GO categories
Total
86736
We further categorized the functions of predicted
secreted fungal proteins using the rpsBLAST tool to
search the Pfam database with a cutoff E-value of
1e-10. Among a total of 93430 predicted secreted
proteins, 43953 protein sequences have a Pfam
match and a total of 880 protein families were
detected. The summary of the Pfam analysis with 33
highly encoded secreted protein families in fungi is
shown in Table 4. A complete list can be
downloaded (http://proteomics.ysu.edu/publicaiton/
data/). The top 10 highly encoded secreted protein
families in fungi were eukaryotic aspartyl protease,
carboxylesterase family, FAD binding domain
containing family, subtilase family, glycosyl
hydrolase family 61, glycosyl hydrolases family
28, glycosyl hydrolases family 18, GMC
oxidoreductase, serine carboxypeptidase, and glycosyl
hydrolase family 3. These proteases identified here
such as aspartyl protease, subtilase, and other
peptidase families are likely to be required for
synergistic degradation of the proteins present in the
various growth medium or substrate materials in the
environments (Druzhinina et al. 2012; Girard et al.
2013). GO analysis and functional domain analysis
are consistent in showing these proteins are mainly
involved in biodegrading complex bio-molecules
including carbohydrates, proteins, lipids, and other
molecules.