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).
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
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)