Sentence examples for metabolic pathways database from inspiring English sources
We thank Hagai Ginsburg for making available the data of the Malaria Parasite Metabolic Pathways database and for valuable advice concerning the metabolism of P. falciparum, Stefan Günther for providing preprocessed data from the SuperTarget database, Nishith Gupta for fruitful discussions with regard to the metabolism of Apicomplexa, and Oliver Frey for proof-reading the manuscript.
Construction of a metabolic pathways database was done using BioCyc [89], in order to compare the different bacteria, C. diphtheriae NCTC 13129, C. efficiens YS-314, C. glutamicum ATCC 13032, and C. jeikeium K411, to the deduced C. pseudotuberculosis pathways.
As a result of this process, kpath (Khaos Metabolic Pathways) database has been published.
The PathCase metabolic pathways database is published [ 12], and we use it as-is in the PathCase-SB.
Functional annotations of the parasite proteins were obtained from PlasmoDB and the Malaria Metabolic Pathways database 47 and those of RBC proteins were retrieved from UniProt database.
The complete genome sequence of sorghum and the SorghumCyc, a metabolic pathways database (http://www.gramene.org/pathway/sorghumcyc.html), as well as next-generation sequencing provide a unique opportunity to obtain more precise information about genes and their networks in sorghum.
Metabolic pathways databases for strains 1002 and C231 were created using the Pathway tools 13 software, developed by SRI International [87].
We first built an initial draft model iAbaylyiv1 using information from the genome annotation, metabolic pathways databases, and the literature.
The available metabolic pathways databases like KEGG [ 22] and BioCyc [ 23] do not capture the compartmentalization of metabolism in eukaryotes and we first attempted to use a protein subcellular localization predictive tool (WPsort, http://wolfpsort.org/)[ 24].
Enzymes from the biochemical pathways of M. tuberculosis from the KEGG metabolic pathway database were compared with proteins from the host H. sapiens, by performing a BLASTp search against the non-redundant database restricted to the H. sapiens subset.
The metabolic pathway database can be accessed online at http://corynecyc.cebio.org.
