An interactive web-based Pseudomonas aeruginosa genome database: Discovery of new genes, pathways and structures

Croft, L; Beatson, SA; Whitchurch, CB; Huang, B; Blakeley, RL; Mattick, JS

An interactive web-based Pseudomonas aeruginosa genome database: Discovery of new genes, pathways and structures

Croft, L Beatson, SA Whitchurch, CB

Huang, B Blakeley, RL Mattick, JS

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Publication Type:: Journal Article
Citation:: Microbiology, 2000, 146 (10), pp. 2351 - 2364
Issue Date:: 2000-01-01

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Field	Value	Language
dc.contributor.author	Croft, L	en_US
dc.contributor.author	Beatson, SA	en_US
dc.contributor.author	Whitchurch, CB https://orcid.org/0000-0003-2296-3791	en_US
dc.contributor.author	Huang, B	en_US
dc.contributor.author	Blakeley, RL	en_US
dc.contributor.author	Mattick, JS	en_US
dc.date.issued	2000-01-01	en_US
dc.identifier.citation	Microbiology, 2000, 146 (10), pp. 2351 - 2364	en_US
dc.identifier.issn	1350-0872	en_US
dc.identifier.uri	http://hdl.handle.net/10453/9467
dc.description.abstract	Using the complete genome sequence of Pseudomonas aeruginosa PAO1, sequenced by the Pseudomonas Genome Project (ftp://ftp.pseudomonas.com/data/pacontigs.121599), a genome database (http://pseudomonas.bit.uq.edu.au/) has been developed containing information on more than 95% of all ORFs in Pseudomonas aeruginosa. The database is searchable by a variety of means, including gene name, position, keyword, sequence similarity and Pfam domain. Automated and manual annotation, nucleotide and peptide sequences, Pfam and SMART domains (where available), Medline and GenBank links and a scrollable, graphical representation of the surrounding genomic landscape are available for each ORF. Using the database has revealed, among other things, that P. aeruginosa contains four chemotaxis systems, two novel general secretion pathways, at least three loci encoding F17-like thin fimbriae, six novel filamentous haemagglutinin-like genes, a number of unusual composite genetic loci related to vgr/RHs elements in Escherichia coli, a number of fix-like genes encoding a micro-oxic respiration system, novel biosynthetic pathways and 38 genes containing domains of unknown function (DUF1/DUF2). It is anticipated that this database will be a useful bioinformatic tool for the Pseudomonas community that will continue to evolve.	en_US
dc.relation.ispartof	Microbiology	en_US
dc.relation.isbasedon	10.1099/00221287-146-10-2351	en_US
dc.subject.classification	Microbiology	en_US
dc.subject.mesh	Fimbriae, Bacterial	en_US
dc.subject.mesh	Pseudomonas aeruginosa	en_US
dc.subject.mesh	Bacterial Proteins	en_US
dc.subject.mesh	Adhesins, Bacterial	en_US
dc.subject.mesh	Amino Acid Sequence	en_US
dc.subject.mesh	Chemotaxis	en_US
dc.subject.mesh	Databases, Factual	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Hemagglutinins	en_US
dc.subject.mesh	Internet	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.title	An interactive web-based Pseudomonas aeruginosa genome database: Discovery of new genes, pathways and structures	en_US
dc.type	Journal Article
utslib.citation.volume	10	en_US
utslib.citation.volume	146	en_US
utslib.for	1108 Medical Microbiology	en_US
dc.location.activity	ISI:000089985400003	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	closed_access
pubs.issue	10	en_US
pubs.publication-status	Published	en_US
pubs.volume	146	en_US

Abstract:

Using the complete genome sequence of Pseudomonas aeruginosa PAO1, sequenced by the Pseudomonas Genome Project (ftp://ftp.pseudomonas.com/data/pacontigs.121599), a genome database (http://pseudomonas.bit.uq.edu.au/) has been developed containing information on more than 95% of all ORFs in Pseudomonas aeruginosa. The database is searchable by a variety of means, including gene name, position, keyword, sequence similarity and Pfam domain. Automated and manual annotation, nucleotide and peptide sequences, Pfam and SMART domains (where available), Medline and GenBank links and a scrollable, graphical representation of the surrounding genomic landscape are available for each ORF. Using the database has revealed, among other things, that P. aeruginosa contains four chemotaxis systems, two novel general secretion pathways, at least three loci encoding F17-like thin fimbriae, six novel filamentous haemagglutinin-like genes, a number of unusual composite genetic loci related to vgr/RHs elements in Escherichia coli, a number of fix-like genes encoding a micro-oxic respiration system, novel biosynthetic pathways and 38 genes containing domains of unknown function (DUF1/DUF2). It is anticipated that this database will be a useful bioinformatic tool for the Pseudomonas community that will continue to evolve.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/9467