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Some of the genes simultaneously expressed by different species shared the same function — for instance, genes associated with growth or respiration.
In our initial attempt, we performed an analysis of the B. subtilis TRN considering only TFs in the absence of any σ factor (data not shown) and found that the resulting network was biologically meaningless because it was decomposed into a very large number of small modules, many of which shared the same function or metabolic process.
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More specifically, orthologs are more likely to share the same function while paralogs can undergo functional shifts.
Ideally, FunFams are groups of protein domains with a high probability of sharing the same function(s) and therefore the functionally important residues (e.g. catalytic residues, ligand-binding residues) in a family are also expected to be highly conserved.
Such groups of homologous proteins sharing the same function will be referred to as functional families hereafter.
So, what is oral history and does it share the same function as today's podcasts?
Whether their homologs share the same function in trafficking in Apicomplexa warrants further interest.
HMMs were built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same protein family.
This allowed an accurate identification of orthologues, which is an essential step of phylogenomic analyses because orthologues are more likely to share the same function than paralogues [11].
All of the proteins from the genome sequence were also searched against the Pfam [39] (release 20.0) HMMs (hmmpfam HMMER version 2.3.2, parameters: -E 0.1 –cut_ga) and TIGRFAMs [40] (release 6.0) built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same family.
The analysis also indicated that some ABC systems may share the same function.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com