  Background: The length of a protein sequence is largely determined by its
function, i.e. each functional group is associated with an optimal size.
However, comparative genomics revealed that proteins length may be affected by
additional factors. In 2002 it was shown that in bacterium Escherichia coli and
the archaeon Archaeoglobus fulgidus, protein sequences with no homologs are, on
average, shorter than those with homologs. Most experts now agree that the
length distributions are distinctly different between protein sequences with
and without homologs in bacterial and archaeal genomes. In this study, we
examine this postulate by a comprehensive analysis of all annotated prokaryotic
genomes and focusing on certain exceptions.
  Results: We compared lengths distributions of having homologs proteins (HHPs)
and non-having homologs proteins (orphans or ORFans) in all currently annotated
completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have
strikingly different length distributions in almost all genomes. As previously
established, the HHPs, indeed, are, on average, longer than the ORFans, and the
length distributions for the ORFans have a relatively narrow peak, in contrast
to the HHPs, whose lengths spread over a wider range of values. However, about
thirty genomes do not obey these rules. Practically all genomes of Mycoplasma
and Ureaplasma have atypical ORFans distributions, with the mean lengths of
ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of
atypical genomes.
  Conclusions: We confirmed on a ubiquitous set of genomes the previous
observation that HHPs and ORFans have different gene length distributions. We
also showed that Mycoplasmataceae genomes have distinctive distributions of
ORFans lengths. We offer several possible biological explanations of this
phenomenon.
