seqinr (version 3.4-5)

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)

Format

A data frame with 20 rows for the amino-acids and the following 7 columns:

aaa

amino-acid (three-letters code).

a

amino-acid (one-letter code).

prec

precursor metabolites (see details).

p

number of high-energy phosphate bonds contained in ATP and GTP molecules.

h

number of available hydrogen atoms carried in NADH, NADPH, and FADH2 molcules.

tot

total metabolic cost assuming 2 high-energy phosphate bonds per hydrogen atom.

gc

an ordered factor (l<m<h) for the G+C class of the amino-acid (see details)

Details

Precursor metabolites are: 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 l<m<h for the gc 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

# NOT RUN {
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\nas function of their G+C class" )
boxplot(aacost$tot~aacost$gc, horizontal = TRUE, add = TRUE)   
# }