seqinr (version 1.0-1)

aacost: Aerobic cost of amino-acids in Escherichia coli and G+C classes

Description

The metabolic cost of amino-acid biosynthesis in E. coli under aerobic conditions from table 1 in Akashi and Gojobori (2002). The G+C classes are from Lobry (1997).

Usage

data(aacost)

source

Akashi, H, Gojobori, T. (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America, 99:3695-3700. Lobry, J.R. (1997) Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene, 205:309-316. Lobry, J.R. (2004) Life history traits and genome structure: aerobiosis and G+C content in bacteria. {Lecture Notes in Computer Sciences}, 3039:679-686.

Details

precursor metabolites: penP, ribose 5-phosphate; PRPP, 5-phosphoribosyl pyrophosphate; eryP, erythrose 4-phosphate; 3pg, 3-phosphoglycerate; pep, phosphoenolpyruvate; pyr, pyruvate; acCoA, acetyl-CoA; akg, alpha-ketoglutarate; oaa, oxaloacetate. Negative signs on precursor metabolites indicate chemicals gained through biosynthetic pathways. Costs of precursors reflect averages for growth on glucose, acetate, and malate (see Table 6 in the supporting information from Akashi and Gojobori 2002). The levels lgc ordered factor stand for Low G+C, Middle G+C, High G+C amino-acid, respectively. The frequencies of Low G+C amino-acids monotonously decrease with G+C content. The frequencies of High G+C amino- acids monotonously increase with G+C content. The frequencies of Middle G+C amino-acids first increase and then decrease with G+C content. These G+C classes are from Lobry (1997). example(aacost) reproduces figure 2 from Lobry (2004).

References

citation("seqinr")

Examples

data(aacost)
levels(aacost$gc) <- c("low G+C", "mid G+C", "high G+C")
stripchart(aacost$tot~aacost$gc, pch = 19, ylim = c(0.5,3.5),
     xlim = c(0, max(aacost$tot)),
     xlab = "Metabolic cost (high-energy phosphate bonds equivalent)",
     main = "Metabolic cost of the 20 amino-acids
as function of their G+C class" )
boxplot(aacost$tot~aacost$gc, horizontal = TRUE, add = TRUE)