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In general, previously selected pathways are displayed by either their KEGG pathway code or full name.
Figure 3 illustrates pathway mapping for the Glycolysis/Gluconeogenesis pathway (KEGG pathway code: 00010) using the ORFeome of L. acidophilus NCFM [ 10] as query set and the complete KEGG database as template.
The 41 essential genes in the cell wall/membrane/envelope biogenesis pathway code for proteins involved in peptidoglycan biosynthesis, LPS core region and lipid-A biosynthesis; proteins for O-antigen biosynthesis were not among the essential genes.
Several genes whose expression is modulated by each pathway code for proteins that could be involved in the regulation of specific physiological and developmental processes in response to environmental signals in this fungal model.
Many genes in this pathway code for histones, but the high DN/DS ratio is caused by other genes, such as BRCA1, MSH4, TOP3A, and PRDM9 (supplementary table S3, Supplementary Material online), some of which were recently reported to be under positive selection (Lou et al. 2014; Schwartz et al. 2014).
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The KEGG pathway codes and names have boldface type.
In addition, we characterize a third neural pathway coding odor repellence.
They suggest that action effect anticipation results in the preactivation of the pathway coding for the expected stimulus.
The numbers of pathway codes sum to more than the total number of included citations because more than one code could be applied to a given citation.
Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction.
The pathway consists in four reactions (arranged in a linear pathway) coded by two genes: BLBBGE_281 [GenBank: CP001487] that codes the enzyme with activity EC 1.3.1.76 and the gene BLBBGE_278 [GenBank: CP001487] which codes an enzyme that catalyzes activities EC 2.1.1.107 and EC 4.99.1.4.
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