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

Description Usage Format Details Source References Examples

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

1

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).

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.

References

citation("seqinr")

Examples

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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)   


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