For example, in Arabidopsis, the family of BAG proteins initially annotated as hypothetical proteins are now annotated as bag gene family members, their function as regulators of apoptosis-like processes has also been characterized.
With the characterization of C02F12.5 ESTs, the gene initially annotated as C02F12.5 in WormBase was subsequently annotated as two separate genes, C02F12.10 and C02F12.5 (Fig. 1).
As a result, only 46 out of the 101 genomic sequences initially annotated as putative nsLtp genes were found to encode proteins displaying the features of plant nsLTPs (Table 1).
2 Hits that involved a majority of nucleotides that were in between annotated ORFs. 3 ORFs that were not initially annotated as transposases of the PSSM IS family but were hits of the PSI-BLAST search.
Deciphering of the P. falciparum genome in 2002 [ 5] revealed 5,300 5,400 genes, 60% of which were initially annotated as hypothetical, since no function could be ascribed to them based on sequence similarity.
The K/P set contains two canonical positive regulators of JAK/STAT signaling with three dsRNAs each: domeless (dome), which was initially annotated as a phosphatase [ 23], and the kinase hopscotch (hop) (reviewed in [ 24]).
Finally, we recorded the transcriptional up-regulation of a gene coding for a protein containing a zinc finger domain that was initially annotated as a metal responsive transcription factor (MTF -1-like protein (Esi0513_0010) under both Cu and oxidative stress.
Despite significant efforts, only three protein-coding genes were so far detected in the mitochondrial genome of E. gracilis, namely subunits 1 through 3 of cytochrome c oxidase (cox1, cox2, and cox3), the latter subunit initially annotated as nad6 (Tessier et al. 1997; Yasuhira and Simpson 1997).
The mapped GO terms were initially annotated with the default annotation threshold (55) and un-annotated sequences were further annotated at a threshold of 45.
For example, although butyrate-CoA ligase (E.C. 6.2.1.2) essential for the utilization of butyrate was not initially annotated, R. eutropha appears to utilize butyrate as a carbon source [ 32, 34].
