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Computational Molecular Biology 2014, Vol. 4, No. 7, 1-17
http://cmb.biopublisher.ca
8
Table 4 Highly encoded secreted protein families in fungi
Pfam ID
Members
%
a
Pfam
Function
pfam00026
1473
3.4
Asp
Eukaryotic aspartyl protease
pfam00135
1419
3.2
COesterase
Carboxylesterase family
pfam01565
1395
3.2
FAD_binding_4
FAD binding domain
pfam00082
1279
2.9
Peptidase_S8
Subtilase family
pfam03443
1150
2.6
Glyco_hydro_61
Glycosyl hydrolase family 61
pfam00295
924
2.1
Glyco_hydro_28
Glycosyl hydrolases family 28
pfam00704
924
2.1
Glyco_hydro_18
Glycosyl hydrolases family 18
pfam05199
873
2.0
GMC_oxred_C
GMC oxidoreductase
pfam00450
845
1.9
Peptidase_S10
Serine carboxypeptidase
pfam00933
809
1.8
Glyco_hydro_3
Glycosyl hydrolase family 3 N terminal
pfam04389
695
1.6
Peptidase_M28
Peptidase family M28
pfam07732
651
1.5
Cu-oxidase_3
Multicopper oxidase
pfam00264
631
1.4
Tyrosinase
Common central domain of tyrosinase
pfam04616
591
1.3
Glyco_hydro_43
Glycosyl hydrolases family 43
pfam01083
569
1.3
Cutinase
Cutinase
pfam09286
519
1.2
Pro-kuma_activ
Pro-kumamolisin
pfam01522
486
1.1
Polysacc_deac_1
Polysaccharide deacetylase
pfam00150
454
1.0
Cellulase
Cellulase (glycosyl hydrolase family 5)
pfam09362
450
1.0
DUF1996
Domain of unknown function (DUF1996)
pfam00328
417
0.9
His_Phos_2
Histidine phosphatase superfamily (branch
pfam00840
410
0.9
Glyco_hydro_7
Glycosyl hydrolase family 7
pfam00188
400
0.9
CAP
Cysteine-rich secretory protein family
pfam01764
397
0.9
Lipase_3
Lipase (class 3)
pfam00544
393
0.9
Pec_lyase_C
Pectate lyase
pfam00331
381
0.9
Glyco_hydro_10
Glycosyl hydrolase family 10
pfam00457
377
0.9
Glyco_hydro_11
Glycosyl hydrolases family 11
pfam01055
366
0.8
Glyco_hydro_31
Glycosyl hydrolases family 31
pfam00246
348
0.8
Peptidase_M14
Zinc carboxypeptidase
pfam12708
337
0.8
Pectate_lyase_3
Pectate lyase superfamily protein
pfam07519
331
0.8
Tannase
Tannase and feruloyl esterase
pfam00722
325
0.7
Glyco_hydro_16
Glycosyl hydrolases family 16
pfam00394
303
0.7
Cu-oxidase
Multicopper oxidase
pfam13668
301
0.7
Ferritin_2
Ferritin-like domain
Note:
a
The percentage (%) was calculated based on a total of 43853 proteins having a Pfam match. The complete list can be
downloaded (see text for details)
3 Discussion
We constructed the fungal protein subcellular location
database and named it Fungal Secretome and
Subcellular Proteome Knowledgebase (FunSecKB2).
Comparing with FunSecKB (Lum and Min 2011), the
number of total protein entries increased from 478,073
in FunSecKB to 1,976,832 in FunSecKB2, and the
number of fungal species including different varieties
and strains having a complete proteome increased
from 52 in FunSecKB to 210 in FunSecKB2. The
subcellular locations in FunSecKB2 were also
expanded to include not only secretomes but also
other subcellular locations including mitochondria,
cytosol (cytoplasm), cytoskeleton, Golgi apparatus,
lysosome, nucleus, peroxisome, plasma membrane
and vacuole. In addition, for the secretomes, we
further classified them as curated, predicted to be
highly likely secreted, likely secreted, and weakly
likely secreted protein subsets. This refinement of
classifications of secreted proteins and other