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Although this mutation is still annotated as one with unknown clinical importance in the BIC database, some studies support that it could be pathogenic [ 20, 27].
The GenBank RNA associated with this gene was altered to remove the frameshift, but it is still annotated as a pseudogene [GenBank:XR_010864.2].
Of the BtuB transporters one is a single gene (all3310), whereas the other (the gene which we confirmed and which is still annotated as alr4028/alr4029) is in a rather typical genomic environment, namely in front of three genes encoding the periplasmic and the plasma membrane localized iron transport machinery.
Analysis of the functional category of the down-regulated genes was shown in Figure 2. The results showed that the most affected functional categories were "hypothetical proteins" and "unknown function", representing a total of more than 68% of all the down-regulated genes, consistent with the fact that nearly half of the Synechocystis genome is still annotated as hypothetical up to now [ 10, 18].
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About one third of the genes of EHEC are still annotated as hypothetical.
Most of them are still annotated as "putative/hypothetical protein", "expressed" protein, "unknown" protein or "stress-responsive" protein.
Especially, some hypothetical genes may have functional counterparts in current databases, whereas they are still annotated as hypothetical.
At the date of writing, the PlasmoDB 5.4 database includes 5 484 coding genes, 3 155 of which (57%) are still annotated as hypothetical.
Furthermore, if the name of a topmost section consisted of two merged concepts, it was still annotated as one section heading.
The high percentage of functionally unknown proteins identified is not unreasonable, considering more than 40% of proteins in the Synechocystis genome are still annotated as hypothetical proteins without any functional prediction.
Functional category analysis of the induced genes showed that the most affected functional categories were "hypothetical proteins", representing a total of more than 40% of all the up-regulated genes, consistent with the fact that nearly half of the genes in the Synechocystis genome are still annotated as hypothetical up to now [ 27].
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