title: Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.
abstract: BACKGROUND
  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. This trend is seen for most of the bacterial and archaeal genomes published to date.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Although 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.
authors.affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark. ljj@cbs.dtu.dk
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.forename: Marie
authors.initials: M
authors.lastname: Skovgaard
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.forename: Merete Kjaer
authors.initials: MK
authors.lastname: Jørgensen
authors.forename: Christiane
authors.initials: C
authors.lastname: Lundegaard
authors.forename: Corinna Cavan
authors.initials: CC
authors.lastname: Pedersen
authors.forename: Nanna
authors.initials: N
authors.lastname: Petersen
authors.forename: David
authors.initials: D
authors.lastname: Ussery
mesh_terms: D000596:Amino Acids / Q000235:genetics / Q000502:physiology; D019843:Archaeal Proteins / Q000235:genetics / Q000502:physiology; D001482:Base Composition; D019641:DNA, Archaeal / Q000032:analysis; D019766:Genes, Archaeal / Q000502:physiology; D020745:Genome, Archaeal; D005810:Multigene Family / Q000235:genetics / Q000502:physiology; D016366:Open Reading Frames / Q000235:genetics / Q000502:physiology; D011237:Predictive Value of Tests; D024363:Transcription Initiation Site
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D019641:DNA, Archaeal