Bioinformatic Protocols and the Knowledge-Base for Secretomes in Fungi

  • Gengkon Lum
  • Xiang Jia Min
Part of the Fungal Biology book series (FUNGBIO)


Fungal secreted proteins play important roles in cell signaling, metabolism, and regulation of fungal growth and development. The secretome refers to all secreted proteins in a proteome that are identified from completely sequenced genomes. The majority of secreted proteins are classical, signal peptide-dependent proteins that can be predicted using bioinformatics tools. In this chapter, we describe some commonly used tools for secreted protein prediction in fungi and propose a relatively accurate bioinformatic protocol for fungal secretome identification. The protocol combines multiple signal peptide or subcellular location predictors, including SignalP, WoLF PSORT, and Phobius, with TMHMM for removing transmembrane proteins and PROSITE PS-Scan for removing endoplasmic reticulum (ER) proteins. Applying this protocol, we have built the fungal secretome knowledge-base (FunSecKB). The utility of FunSecKB is described in detail. FunSecKB serves the community as a central portal for search and deposition of fungal secretome information.


Secreted proteins Secretome Signal peptide Fungi Prediction Knowledge-base Database 



We thank Dr. Gary Walker for his mentoring support and Jessica Orr for assistance in manual data curation. The work is supported by Youngstown State University (YSU) Research Council (Grants 2009-10 #04-10 and 2010-2011 #12-11), YSU Research Professorship (2009–2011), and the College of Science, Technology, Engineering, and Mathematics Dean’s reassigned time for research to XJM.


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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA
  2. 2.Department of Biological Sciences, Center for Applied Chemical BiologyYoungstown State University, One University PlazaYoungstownUSA

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