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Further, this analysis provides important novel information, with respect to the T. gondii proteome, since 3,838 (60%) of the experimentally identified proteins have been annotated as "hypothetical", "putative" or "predicted" in the NCBI NR database.
These loci represent highly conserved proteins that have been annotated as hypothetical proteins.
Many proteins in this category have been annotated as hypothetical proteins, PPE and mammalian cell entry (mce) family virulence proteins.
Thirty-three proteins have been annotated as hypothetical proteins in the M. tuberculosis genome from NCBI; these also appeared in the PPI networks (Fig. 1B) (also see Additional file 3).
In the end, a total of 232 orthologous genes, including 225 genes that have clear functional definition and 7 genes that have been annotated as hypothetical proteins (Additional file 2 Table S2), were used to reconstruct LAB phylogeny in this study.
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Genes that are annotated as hypothetical as well as those that are not present in strain HK1651 were then blasted against Genbank non-redundant protein sequence database.
These windows contain 1,290 annotations which in turn are largely conserved across Tbb/Tbr/Tbg2, although 69.6% are annotated as hypothetical coding regions or miscellaneous annotations yet to be characterized.
Due to the limitations of annotation pipelines, the majority of genes encoded by pSC2 are annotated as hypothetical genes with no conclusive function or experimentally characterized homologs.
In total, 12 proteins were annotated as hypothetical proteins.
Significantly, 50% of the targets were annotated as hypothetical proteins.
Four localized GFP fusion proteins were annotated as hypothetical or conserved hypothetical proteins, in addition to CC2362.
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