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Comparison of methods was carried out across 11 genes encoding for products ranging from multi-domain proteins with regions of poor conservation to single-copy, highly conserved housekeeping proteins (Table 1).
Moreover, the more species we combine the more we focus our prediction on evolutionary conserved functions, which becomes clear when studying predictions for highly conserved housekeeping functions (see Discussion).
The first, introduced by Nakano et al. in 2007, consists of 8 conserved housekeeping genes.
This point bears special relevance in the case of genotypic taxonomy, which is based on the application of conserved housekeeping genes as markers.
These probes corresponded to either highly conserved housekeeping genes (i.e. encoding ribosomal proteins), or to genes potentially involved in horizontal gene transfer events (many of these were prophage and transposon-related).
The ortholog relationship between A. pleuropneumoniae and other species within the family Pasteurellaceae was consistent with their phylogenetic relationship based on the sequence analyses of 16S rRNA [17] and 50 highly conserved housekeeping genes [18].
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In this work, unlike the other C. trachomatis MLST schemes, we used complete genomic comparisons of 7 strains from 4 species within the family Chlamydiaceae to identify conserved candidate housekeeping genes across the genomes.
Autophagy is an evolutionarily conserved cellular housekeeping process that removes damaged organelles and protein aggregates that are unnecessary or dysfunctional to the cells by delivering cytoplasmic substrates to lysosomes for degeneration.
Although the W-dyad is universally conserved in housekeeping σ's (Gruber and Bryant, 1997), it is not a conserved feature of alternative σ's (Lonetto et al., 1992; Helmann, 2002; Campbell et al., 2003); bulky hydrophobic residues are favored at the corresponding positions of alternative σ's (but rarely W).
Malaria proteins contain amino acid sequences highly conserved in human housekeeping proteins [233], implying the pre-existence of malaria-cognate nTregs.
MiRNAs commonly have non-related targets and are frequently involved in housekeeping conserved pathways.
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