As a source of reliable human protein pathway information we utilized 913 annotated pathways from the Pathway Interaction Database [22].
While Rho and BR share a light-driven isomerization event in the excited state, they may utilize different relaxation pathways from the Franck Condon state.
As shown in Fig. 3, the reconstructed central metabolic pathways from the D. desulfuricans genome certainly showed that these organic acids could be utilized as energy and carbon sources via the oxidative tricarboxylic acid (TCA) cycle and various anaplerotic pathways.
Three routes exist for the maintenance of proper intracellular nucleotide pools: a) de novo biosynthesis, which requires folate cofactors and is restricted to selected cell types; b) the salvage pathway, which utilizes intermediates from the degradation pathway of nucleotides; and c) influx of nucleosides from the extracellular milieu.
Note that vacuole biogenesis utilizes at least three direct transport pathways: autophagy/Cvt (from the cytoplasm), AP-3/ALP (from the Golgi), and CPY (from the MVB/endosome) pathways (Bryant and Stevens, 1998; Hecht et al., 2014).
The pathway from aspartate utilizes the first two enzymes (EC:2.7.2.4 and EC:1.2.1.11) of the DAP pathway from lysine synthesis for the production of aspartate semialdehyde.
We have developed a system, PWTEES, which extracts pathway interactions from the literature utilizing an existing event extraction tool (TEES) and pathway named entity recognition (PathNER).
DIANA mirPath v2.0 web-application [ 21] and overrepresentation analysis (ORA) tool available in ConsensusPathDB (http://cpdb.molgen.mpg.de/CPDB) [ 22] were utilized in order to identify pathways from Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg/) enriched among the list of mRNA targets regulated by each selected miRNA.
The sulfur assimilation pathway also varies among propionibacteria, with species utilizing from the most oxidized sources (sulfate) to the most reduced ones (sulfide) [ 53].
The serine/threonine kinase Akt (PKB) is utilized in a variety of signaling pathways from T cell growth factors such as IL-7R, and CD28 co-stimulatory signal [ 4, 5].
