An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

Table 1 Proteome size and single signalP3 signal peptide and signal anchor predictions of four selected Aspergillus species

Species	A. niger CBS 513.88	A. niger ATCC 1015	A. oryzae RIB40	A. fumigatus Af293	A. nidulans FGSC A4
protein CDS	14086*	11197**	10406**	9887**	10665**
signalP3 NN	1831	1540	1751	1258	1469
signalP3 HMM SP	2016	1687	1802	1067	1612
signalP3 HMM SA	627	529	582	391	488

Species are ranked by their phylogenetic distance to A. niger CBS 513.88
NN, neural network method (proteins were considered to be SP proteins if the signalP3 D-score >0.43); HMM, hidden Markov model; SP, signal peptide; SA, signal anchor
* Number obtained from the Refseq section of GenBank
** Numbers obtained from http://www.broad.mit.edu/annotation/genome/aspergillus_group/MultiHome.html

ISSN: 1471-2164