aacost                package:seqinr                R Documentation

_A_e_r_o_b_i_c _c_o_s_t _o_f _a_m_i_n_o-_a_c_i_d_s _i_n _E_s_c_h_e_r_i_c_h_i_a _c_o_l_i _a_n_d _G+_C _c_l_a_s_s_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     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).

_U_s_a_g_e:

     data(aacost)

_F_o_r_m_a_t:

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

     _a_a_a amino-acid (three-letters code).

     _a amino-acid (one-letter code).

     _p_r_e_c 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.

     _t_o_t total metabolic cost assuming 2 high-energy phosphate bonds
          per hydrogen atom.

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

_D_e_t_a_i_l_s:

     precursor metabolites: penP, ribose 5-phosphate; PRPP,
     5-phosphoribosyl pyrophosphate; eryP, erythrose 4-phosphate; 3pg,
     3-phosphoglycerate; pep, phospho_enol_pyruvate; 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).

_S_o_u_r_c_e:

     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.

_R_e_f_e_r_e_n_c_e_s:

     'citation("seqinr")'

_E_x_a_m_p_l_e_s:

     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)   

