However, the tblastn search also missed homologues.
Ultimately, even at the highest E-value cutoff the tblastn analysis missed homologues.
Our results indicate that Blast, at least when applied within eukaryotes, only misses homologues of extremely fast-evolving sequences, which are rare in the mammalian genome, as well as sequences evolving homogeneously or pseudogenes.
The tblastn screen yielded more positives, due to the fact that the HMM-based method missed homologues that are too divergent to give a significant Pfam result or are encoded outside of cydAB operons (Additional files 1 and 2a).
Finally, position-specific search implemented in PSI-BLAST [ 50] was used to search for possible missed homologues among the annotated genes from human, mouse, rat and Drosophila genomes and a ScanProsite [ 51] search of all genes in the UniProt (Swiss-Prot and TrEMBL) [ 52] and PDB [ 53] databases.
Of the 273 genes we removed 26 genes due to gene symbol overlap, missing human homologue or missing ensembl ID.
Plants and fungi are also missing the PARP4 homologue.
Furthermore, the putative not processed intron includes a stop codon rendering a truncated E2 homologue, missing the active cysteine residue site, which may block ubiquitin transfer.
This and the missing of a homologue of APS kinase clearly indicate that CysH acts as APS reductase in C. glutamicum, corroborating the prediction made by Lee [ 26].
Both proteins share the same region on Arabidopsis chromosome 4 and TEBICHI has a helicase domain at 490 890aa and a polymerase domain at 1700 2150aa; furthermore, this N-terminal portion is missing in animal homologues of TEB protein, MUS308/POLQ (Dr. Soichi Inagaki, personal communication).
