Please note that we will be retiring this old site on Tuesday, August 25th, 2015.
At that point, the URL for www.pseudomonas.com will bring you to our new site currently hosted at beta.pseudomonas.com. We encourage you to visit the new site now and see a more recent set of updated gene annotations and MANY more Pseudomonas strains.
Pseudomonas Genome Database - Supplementary Data

Supplementary Data

Important Note

The data listed on this page is supplementary to the original genome annotations associated with the first Pseudomonas aeruginosa genome publication by Stover et al. ( Nature 406:959-964. 2000). For the most up to date annotations, please see the continually updated database.

Correction to Stover et al. Nature 406:959-964 (2000).

  • A typographical error was made on page 959.  The inversion region between rrnA and rrnB spans 2.2 Mbp.

Genome-wide analyses

  • Linear map of the genome. The 5570 genes, color-coded by functional category.

  • Restriction analysis of genomic DNA. The assembled DNA sequence differs from the published physical map of PAO1 in that over one-quarter of the genome is inverted. Restriction analysis was consistent with the interpretation that this inversion was the result of recombination the rrnA and rrnB ribosomal RNA loci.

  • Regions of atypical G+C content. The PAO1 genome has an overall G+C content of 66.6%. However, we noted isolated regions with lower G+C content. These regions often had atypical codon usage and may be the result of recent horizontal transfer.

Comparisons of the sequences of P. aeruginosa ORFs with ORFs of other organisms

The PAO1 genome is more than a third larger than that of E. coli K12. Several analyses suggested that P. aeruginosa 's large genome is the result of greater genetic complexity rather than differences in genome organization or extensive gene duplication.

Identification of genes belonging to known families

  • Regulator motifs in the P. aeruginosa genome and four comparative genomes. Over five-hundred genes contain motifs characteristic of transcriptional regulators or of environmental sensors; an additional 13 genes have been demonstrated to encode transcriptional regulators, but lack well-characterized motifs. When homologous families of transcriptional regulators (determined by motif searching) were compared with other bacterial systems, the most striking over-representations in P. aeruginosa were observed in the LysR, AraC, sigma-ECF, LuxR and two-component regulator families. There is an extraordinary number of putative two-component regulators, with 55 sensor proteins, 89 response regulators and 14 sensor/response regulator hybrids, more than twice the number found in E. coli and B. subtilis.

  • Phylogenetic analysis of the OprM superfamily outer membrane proteins. PAO1 contains approximately 150 genes for outer membrane proteins, substantially more than other sequenced genomes. 18 of these belong to the OprM family and are thought to be involved in efflux or secretion. Additional information on P. aeruginosa outer membrane proteins.

  • Substrate specificity of predicted transporters.  P. aeruginosa has nearly 300 cytoplasmic membrane transport systems. The predicted substrate specificities of these transporters are compared to those of E. coli, B. subtilis, and M. tuberculosis. Additional information on genomic comparisons of membrane transport systems.

Genetic loci that encode novel pathways or systems.

About 30% of PAO1 ORFS could be assigned a probable function based on similarity to established sequence motifs, but could not be assigned a definite name. During annotation we noted that some of these genes were in clusters for which a collective function could be proposed—for example, the finding of adjacent genes encoding an RND-type transport protein, a probable RND membrane fusion protein, and an OprM-family outer membrane protein suggests that these gene products work together to export some undetermined substrate.