Article

An analysis of the Candida albicans genome database for soluble secreted proteins using computer-based prediction algorithms.

Infectious Diseases Section, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
Yeast (impact factor: 1.89). 06/2003; 20(7):595-610. DOI:10.1002/yea.988 pp.595-610
Source: PubMed

ABSTRACT We sought to identify all genes in the Candida albicans genome database whose deduced proteins would likely be soluble secreted proteins (the secretome). While certain C. albicans secretory proteins have been studied in detail, more data on the entire secretome is needed. One approach to rapidly predict the functions of an entire proteome is to utilize genomic database information and prediction algorithms. Thus, we used a set of prediction algorithms to computationally define a potential C. albicans secretome. We first assembled a validation set of 47 C. albicans proteins that are known to be secreted and 47 that are known not to be secreted. The presence or absence of an N-terminal signal peptide was correctly predicted by SignalP version 2.0 in 47 of 47 known secreted proteins and in 47 of 47 known non-secreted proteins. When all 6165 C. albicans ORFs from CandidaDB were analysed with SignalP, 495 ORFs were predicted to encode proteins with N-terminal signal peptides. In the set of 495 deduced proteins with N-terminal signal peptides, 350 were predicted to have no transmembrane domains (or a single transmembrane domain at the extreme N-terminus) and 300 of these were predicted not to be GPI-anchored. TargetP was used to eliminate proteins with mitochondrial targeting signals, and the final computationally-predicted C. albicans secretome was estimated to consist of up to 283 ORFs. The C. albicans secretome database is available at http://info.med.yale.edu/intmed/infdis/candida/

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Keywords

47 C. albicans proteins
 
495 deduced proteins
 
C. albicans secretome database
 
Candida albicans genome database
 
CandidaDB
 
certain C. albicans secretory proteins
 
deduced proteins
 
encode proteins
 
entire proteome
 
extreme N-terminus
 
final computationally-predicted C. albicans secretome
 
N-terminal signal peptide
 
N-terminal signal peptides
 
non-secreted proteins
 
potential C. albicans secretome
 
secreted proteins
 
SignalP version 2.0
 
single transmembrane domain
 
transmembrane domains
 
utilize genomic database information