Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Larimer, Frank W.; Chain, Patrick; Hauser, Loren; Lamerdin, Jane E.; Malfatti, Stephanie; Do, Long; Land, Miriam; Pelletier, Dale A.; Beatty, Thomas G.; Lang, Andrew S.; Tabita, F. Robert; Gibson, James W.; Hanson, Thomas E.; Bobst, Cedric E.; Torres, Janelle L. Torres y; Peres, Caroline; Harrison, Faith H.; Gibson, Jane; Harwood, Caroline S.

doi:10.1038/nbt923

Cited by 677 publications

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“…The 4833 ORFs of Rhodopseudomonas palustris [22]°were°added°to°the°database°to°act°as distracters during identification of the protein standard mixture. For proteomic identification, a database°of°4798°ORFs°from°Shewanella oneidensis [23,°24] was augmented with 44 sequences for immunoglobulins, proteases, keratins, and other proteins.…”

Section: Database Search Configurationmentioning

confidence: 99%

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

Tabb

Thompson

Khalsa-Moyers

et al. 2005

J. Am. Soc. Mass Spectrom.

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Shotgun proteomics experiments require the collection of thousands of tandem mass spectra; these sets of data will continue to grow as new instruments become available that can scan at even higher rates. Such data contain substantial amounts of redundancy with spectra from a particular peptide being acquired many times during a single LC-MS/MS experiment. In this article, we present MS2Grouper, an algorithm that detects spectral duplication, assesses groups of related spectra, and replaces these groups with synthetic representative spectra. Errors in detecting spectral similarity are corrected using a paraclique criterion-spectra are only assessed as groups if they are part of a clique of at least three completely interrelated spectra or are subsequently added to such cliques by being similar to all but one of the clique members. A greedy algorithm constructs a representative spectrum for each group by iteratively removing the tallest peaks from the spectral collection and matching to peaks in the other spectra. This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides. (J Am Soc Mass Spectrom 2005, 16, 1250 -1261

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Section: Database Search Configurationmentioning

confidence: 99%

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

Tabb

Thompson

Khalsa-Moyers

et al. 2005

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…Purple non-sulfur bacteria have been used very successfully in treating swine waste water from piggeries (Kim and Lee, 2000;Kim et al, 2009). Studies show that these bacteria can remove or detoxify many organic compounds, organic acids, COD and phosphate , Larimer et al, 2004. They have a wider range of nutrition than nearly all other microbes and so are able to grow on virtually any organic material with the notable exception of cellulose (Larimer et al, 2004, KEGG, 2013.…”

Section: Statement Of the Problemmentioning

confidence: 99%

“…It was found that Rhodopseudomonas successfully broke down sugars, carbohydrates, lipids and proteins of the food waste and significantly reduced BOD and COD. The microbe in project was Rhodopseudomonas palustris (CGA 009) (Larimer et al, 2004;Ritchie and Runcie, 2013). The advantage of using this strain of Rhodopseudomonas was that it is the same strain, from the same laboratory as that used by Larimer, et al (2004) for sequencing Rhodopseudomonas palustris…”

Section: Scopementioning

confidence: 99%

“…Studies show that these bacteria can remove or detoxify many organic compounds, organic acids, COD and phosphate , Larimer et al, 2004. They have a wider range of nutrition than nearly all other microbes and so are able to grow on virtually any organic material with the notable exception of cellulose (Larimer et al, 2004, KEGG, 2013. It is proposed in this project to investigate the use of photosynthetic bacteria to break down food waste under anaerobic conditions.…”

Section: Statement Of the Problemmentioning

confidence: 99%

“…R. palustris can produce hydrogen gas from palm oil milling effluent which has a very high oil and fatty acid content (VFAs-Volatile Fatty Acids) (Suwansaard et al, 2009). There are very few organic compounds which Rhodopseudomonas cannot use as a carbon source (Larimer et al, 2004;KEGG, 2013). …”

Section: Statement Of the Problemmentioning

confidence: 99%

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Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Cited by 677 publications

References 50 publications

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

Breakdown of food waste by anaerobic fermentation and non-oxygen producing photosynthesis using a photosynthetic bacterium

Clock Evolution and Adaptation: Whence and Whither?

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