Abstract
BackgroundFor most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date.ResultsIn contrast we have found that a large fraction of the genes coding for such orphan proteins in the Methanopyrus kandleri AV19 genome occur within two large regions. These genes have no known homologs except from other M. kandleri genes. However, analysis of their lengths, codon usage, and Ribosomal Binding Site (RBS) sequences shows that they are most likely true protein coding genes and not random open reading frames.ConclusionsAlthough these regions can be considered as candidates for massive lateral gene transfer, our bioinformatics analysis suggests that this is not the case. We predict many of the organism specific proteins to be transmembrane and belong to protein families that are non-randomly distributed between the regions. Consistent with this, we suggest that the two regions are most likely unrelated, and that they may be integrated plasmids.
Highlights
For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins
BLASTP searches of all predicted protein sequences in the M. kandleri genome were performed against a number of different databases
To rule out that the genes within these regions are missing from the databases mentioned above, a TBLASTN search was performed against all sequences in GenBank
Summary
For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. For a newly sequenced genome the number of unique genes is mentioned This is usually claimed to be about one third of the annotated genes. We have discovered that a significant fraction of these genes are located within two large regions of the chromosome (see Figure 1) This is in constrast to what is (page number not for citation purposes)
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