The Pyrobaculum aerophilum str. IM2 genome is 2.22 Million bp long and contains approximately 2706 predicted genes. P. aerophilum is a hyperthermophilic crenarchaeon which was isolated from a boiling marine hole at Martoni Beach, Italy. It grows optimally at 100 C, either in the presence of low amounts of oxygen or anaerobically. It is remarkable for being able to utilize five different oxidants in respiration: oxygen, nitrate, arsenate, selenate, iron (III), and thiosulfate. The genome was sequenced and annotated as the PhD project of Sorel Fitz-Gibbon, a student in Jeffrey Miller's lab.

The sequence was released Dec 2001 by the UCLA/CalTech, and was described in Proc Natl Acad Sci U S A 99:984-9 (2002) Fitz-Gibbon ST, Ladner H, Kim UJ, Stetter KO, Simon MI, et al.  "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. "
Abstract: We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum aerophilum, a facultatively aerobic nitrate-reducing hyperthermophilic (T(opt) = 100 degrees C) crenarchaeon. Clues were found suggesting explanations of the organism's surprising intolerance to sulfur, which may aid in the development of methods for genetic studies of the organism. Many interesting features worthy of further genetic studies were revealed. Whole genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps all crenarchaea) lack 5' untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine-Dalgarno)-based mechanism for translation initiation at the 5' end of transcripts. Inspection of the lengths and distribution of mononucleo... [Click above reference link for full abstract]

Sample position queries

A genome position can be specified by chromosomal coordinate range, COG ID, or keywords from the GenBank or TIGR description of a gene. The available chromosome/plasmid names are:

Browser Chrom/Plasmid NameLength (bp)GC Content (%)Gene CountNCBI RefSeq Accession
chr222243051.362706NC_003364

The following list shows examples of valid position queries for this genome: 

Request:Genome Browser Response:
chrDisplays the entire sequence "chr" in the browser window
chr:1-10000    Displays first ten thousand bases of the sequence "chr"
transporter    Lists all genes with "transporter" in the name or description
PAE0014Display genome at position of gene PAE0014


Credits

The Archaeal Genome Browsers at UCSC were developed by members of the Lowe Lab (Kevin Schneider, Katherine Pollard, Andy Pohl, Todd Lowe) and Robert Baertsch, with significant support from the UCSC Human Genome Browser group. The Archaeal Browsers are run by a slightly modified version of the UCSC Human Genome Browser system. All queries, bug reports, content corrections, suggested improvements, and new track data submissions should be sent to Todd Lowe (lowe @soe.ucsc.edu).

If you use the browser in your published research, please cite our publication in the Nucleic Acids Research Database Issue. Citations and positive feedback will help us obtain funding to continue development of this community resource.