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The 20 pathways were assembled from the Ingenuity Pathway databases and the SuperArray cancer pathway array annotations.
Lists of genes (that is, gene sets) that represent various biological pathways were assembled from the literature.
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Using 69% of all available building blocks, 2597 length-four pathways are assembled, starting from 245 substrates.
Given protein-protein interaction (PPI) data signaling pathways are assembled without knowledge of the intermediate signaling proteins while maximizing the overall probability of the pathway.
The genes in each pathway were assembled manually from literature information as of February 2007.
In Chinese bayberry, the sequences for all 9 genes in the S-W pathway were assembled; however, this was not the case for the other three pathways (Additional File 5).
Finally, a de novo MA biosynthetic pathway is assembled by integrating the established SA biosynthesis and degradation modules.
Herein, to endow Escherichia coli with the ability to utilize methanol, an artificial linear methanol assimilation pathway was assembled in vivo for the first time.
Hence, this metabolic pathway might have been assembled long before the appearance of the LUCA (Brilli and Fani 2004a, b; Fani et al. 1994, 1995; Alifano et al. 1996; Fondi et al. 2009b), but once the entire pathway was assembled, it underwent major rearrangements during evolution, as suggested by the wide variety of different clustering strategies of his genes that has been documented.
According to the model proposed (Fani et al. 2007; Fondi et al. 2009b) on the basis of the available data, it has been suggested that the complete histidine biosynthetic pathway was assembled long before the appearance of the LUCA, which possessed mono-functional his genes.
The previously characterized napyradiomycin (nap) pathway was assembled with the aid of the published sequence [ 14].
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