uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Analysis of two large functionally uncharacterized regions in theMethanopyrus kandleri AV19 genome
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
Show others and affiliations
2003 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 4, 12- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2003. Vol. 4, 12- p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-65231DOI: 10.1186/1471-2164-4-12ISI: 000183126000001PubMedID: 12697059OAI: oai:DiVA.org:uu-65231DiVA: diva2:93142
Available from: 2008-10-17 Created: 2008-10-17 Last updated: 2010-10-19Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed
By organisation
Division of Pharmacognosy
In the same journal
BMC Genomics
Natural Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 188 hits
ReferencesLink to record
Permanent link

Direct link