Statistics of <i>Pneumocystis</i> spp. nuclear and mitochondrial genomic assemblies^a.

a<p>The data of the nuclear genomes are from Cissé et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004425#ppat.1004425-Ciss1" target="_blank">[3]</a>, except those of <i>P. murina</i> which are from <a href="http://broadinstitute.org" target="_blank">broadinstitute.org</a>. The data of the mitochondrial genomes are from Sesterhenn et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004425#ppat.1004425-Sesterhenn1" target="_blank">[4]</a> and Ma et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004425#ppat.1004425-Ma1" target="_blank">[5]</a>.</p>b<p>The nuclear assemblies of the three species are considered to be incomplete and do not include repetitive elements.</p>c<p>The numbers for <i>P. jirovecii</i> and <i>P. carinii</i> overestimate proteome size because some peptides are from incomplete coding DNA sequences at ends of contigs.</p>d<p>Only complete copies in <i>P. carinii</i> assembly were considered.</p><p>Statistics of <i>Pneumocystis</i> spp. nuclear and mitochondrial genomic assemblies^{<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004425#nt101" target="_blank">a</a>}.</p

Some features of selected microorganisms with various lifestyles.

<p>Some features of selected microorganisms with various lifestyles.</p

Some features of free-living microorganisms and obligate parasites.

<p>Some features of free-living microorganisms and obligate parasites.</p

Number of enzymes dedicated to the biosyntheses of amino acids identified in <i>P. carinii</i> and <i>S. pombe</i>^a.

a<p>The reference gene numbers of <i>S. pombe</i> are those obtained from KEGG.</p>b<p>The four enzymes are the same for Ile and Val syntheses.</p>c<p>One of the enzymes is also involved in Ile and Val syntheses.</p

Estimation of the quality of the mapping onto KEGG maps by performing a re-prediction of the annotation of <i>S. pombe</i> proteome through intermediary data set consisting of one, two, three, or 18 fungal proteomes.

<p>The KO - <i>S. pombe</i> association pairs obtained by “blasting” an intermediary data set were evaluated <i>a posteriori</i> as true positive (TP) or false positive (FP) according to the KO - <i>S. pombe</i> mapping which is provided by KEGG. Those missed KO - <i>S. pombe</i> pairs existing in KEGG were taken as false negatives (FN). The overall quality of the obtained mapping can be expressed in terms of precision TP/(TP+FP) and recall TP/(TP+FN).</p

Proteomes investigated for transfer the KEGG annotations of the <i>P. carinii</i> predicted proteome.

<p>Proteomes investigated for transfer the KEGG annotations of the <i>P. carinii</i> predicted proteome.</p