Nucleic Acids Res. 2004 Dec 1;32(21):6321-6. Print 2004.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.

Source

EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max-Delbrueck-Centrum, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany. doerks@embl.de <doerks@embl.de>

Abstract

Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45,110 proteins, 1738 groups could be linked to functionally associated partners. In many cases, those partners are uncharacterized themselves (hinting at newly identified modules) or have been described in general terms only. However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins).

PMID:: 15576358; [PubMed - indexed for MEDLINE]
PMCID:: PMC535681

Free PMC Article

Images from this publication.See all images (2) Free text

MeSH Terms, Substances

MeSH Terms

Substances

Bacterial Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Save items

Related citations in PubMed

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. [Nucleic Acids Res. 2008]
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.
Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, Moreno-Hagelsieb G, Merino E. Nucleic Acids Res. 2008 Jul 1; 36(Web Server issue):W176-80. Epub 2008 May 29.
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. [Nucleic Acids Res. 2006]
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessières P, et al. Nucleic Acids Res. 2006; 34(12):3533-45. Epub 2006 Jul 19.
Review Global analysis of bacterial transcription factors to predict cellular target processes. [Trends Genet. 2004]
Review Global analysis of bacterial transcription factors to predict cellular target processes.
Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P. Trends Genet. 2004 Mar; 20(3):126-31.
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. [Genome Res. 2000]
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.
Huynen M, Snel B, Lathe W 3rd, Bork P. Genome Res. 2000 Aug; 10(8):1204-10.
Review 'Conserved hypothetical' proteins: prioritization of targets for experimental study. [Nucleic Acids Res. 2004]
Review 'Conserved hypothetical' proteins: prioritization of targets for experimental study.
Galperin MY, Koonin EV. Nucleic Acids Res. 2004; 32(18):5452-63. Epub 2004 Oct 12.

See reviews... See all...

Cited by 11 PubMed Central articles

Hot transcriptomics. [Archaea. 2011]
Hot transcriptomics.
Walther J, Sierocinski P, van der Oost J. Archaea. 2011 Feb 7; 2010:897585. Epub 2011 Feb 7.
Analysis of casein alpha S1 & S2 proteins from different mammalian species. [Bioinformation. 2010]
Analysis of casein alpha S1 & S2 proteins from different mammalian species.
Masoodi TA, Shafi G. Bioinformation. 2010 Mar 31; 4(9):430-5. Epub 2010 Mar 31.
Signature proteins for the major clades of Cyanobacteria. [BMC Evol Biol. 2010]
Signature proteins for the major clades of Cyanobacteria.
Gupta RS, Mathews DW. BMC Evol Biol. 2010 Jan 25; 10:24. Epub 2010 Jan 25.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Functional clues for hypothetical proteins based on genomic context analysis in ...
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Nucleic Acids Res. 2004 Dec 1 ;32(21):6321-6. Print 2004 .

PubMed
The apoB/apoA-I ratio is better than the cholesterol ratios to estimate the bala...
The apoB/apoA-I ratio is better than the cholesterol ratios to estimate the balance between plasma proatherogenic and antiatherogenic lipoproteins and to predict coronary risk.
Clin Chem Lab Med. 2004 ;42(12):1355-63.

PubMed
A humanized monoclonal antibody targeting Staphylococcus aureus.
A humanized monoclonal antibody targeting Staphylococcus aureus.
Vaccine. 2004 Dec 6 ;22 Suppl 1:S39-43.

PubMed
Structural basis for the activity of drugs that inhibit phosphodiesterases.
Structural basis for the activity of drugs that inhibit phosphodiesterases.
Structure. 2004 Dec ;12(12):2233-47.

PubMed
Hidden localization motifs: naturally occurring peroxisomal targeting signals in...
Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins.
Genome Biol. 2004 ;5(12):R97. Epub 2004 Nov 30 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: