Table 8

The genes composing the complete ethanol and non-ethanol signatures (see Tables 6 and 7) are organized here by functional groups as described by Riley and Serres [20].

Functional Group

Gene Name


Known Functions (92, 100%)


Carbon compound catabolism (4/4%)

nagA mhpB;

    bglA alsE

Central intermediary metabolism (6/7%)

tktB speD ylbC sfcA cpsB;

    tktA

Energy metabolism (3/3%)

nrfG hyfD;

    nrfE

Amino acid biosynthesis (3/3%)

argH;

    leuA trpD

Cofactors and prosthetic groups (6/7%)

moaE grxB hemX nadB;

    gshA

Lipid metabolism (1/1%)

plsC

Transport (13/14%)

mngA amtB glvC livJ mtlA uhpT livK fes;

    cvrA feoB nagE kdpB betT

Cell processes (10/11%)

fliF zipA xerC fliG tolB;

    pqiB aidB norV amiA hscC

Cell structure (5/5%)

mepA nlpC fhuA ynfA;

    dsbC

Regulatory function (15/16%)

wzzB uidR hcaR nagC hnr cbl lysR rstA gcvA pspF;

    evgS arcB gppA cyaA lon

DNA replication, repair, modification (7/8%)

yaiD xthA topB uvrC parC tus;

    dnaN

Transcription/RNA processing/degradation (4/4%)

pnp dbpA;

    rne deaD

Translation/post-translational modification (12/13%)

aat mnmE;

    tufA fusA rplO tufB alaS rplD rplX glnS infC rplP

Phage, transposon, or plasmid (3/3%)

ydaP intA ylbF

Putative Functions (59, 100%)

General (21/36%)

yfeA ycbX ydhS yibN yagX yeiQ yiaL yhhX yneB yccU ycdJ yhiI yciQ yggF ycdI ybdL ybfL;

    ygjK ynfE yphG ygbE

Cell processes an energy metabolism (1/2%)

caiA

Cell structure (1/2%)

yebU

Central intermediary metabolism (1/2%)

sgbU

Carbon catabolism (1/2%)

ydiF

Nucleotide biosynthesis (1/2%)

hyuA

Transport (7/12%)

fdrA yheH yhiP ybhS ybgH;

    ybbA yejA

Regulation (26/44%)

ygfZ yhfR ybhD ycfX yeeY yiaJ kdgR yfeR ygbI ypdC ydhB yhaJ uvrY yidL recX nanR yidF ycgE yfcD ydcI ygcP ybjN yidP;

    yehI yehU yfiE

Hypothetical Functions (26, 100%)

yaiY ydcK ychA ydfU yqcD yagB ybgI ydfP yjcZ yhcP yaeJ yagR yagZ yaeQ ydiU yhaM ydfE ytfM ynjH ynfC ybfO;

    ybhH ybeQ yqjI yoaD yhgF


A semicolon separates the two groups of genes and those corresponding to the non-ethanol signature are underlined. The composition of the groups was updated using the latest information available in the literature [21-43]. Functional groups were organized in three categories: (1) known functions, (2) putative functions, and (3) hypothetical functions. The putative category was subdivided according to the specific putative function of each gene. Numbers in parenthesis are the total number of genes identified for the functional group and the percentage they represent respect to the total number of genes identified for the category, respectively.

Rollins et al. BMC Bioinformatics 2006 7:377   doi:10.1186/1471-2105-7-377

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