A functional update of the Escherichia coli K-12 genome

View/ Open
Date
2001-08-20Author
Serres, Margrethe H.
Concept link
Gopal, Shuba
Concept link
Nahum, Laila A.
Concept link
Liang, Ping
Concept link
Gaasterland, Terry
Concept link
Riley, Monica
Concept link
Metadata
Show full item recordCitable URI
https://hdl.handle.net/1912/106As published
https://doi.org/10.1186/gb-2001-2-9-research0035DOI
10.1186/gb-2001-2-9-research0035Keyword
Escherichia coli K-12Abstract
Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional
functional information based on biological characterization and functions of sequence-similar
proteins has become available. On the basis of this new information, an updated version of the
annotated chromosome has been generated.
Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116
RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession
U00096 were used. Some protein-coding sequences are compound and encode multimodular
proteins. The coding sequences (CDSs) are represented by modules (protein elements of at
least 100 amino acids with biological activity and independent evolutionary history). There are
4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5%
have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only
7% of the modules appear unique to E. coli, and this number is expected to be reduced as more
genome data becomes available. The imputed functions were assigned on the basis of manual
evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome
annotation system.
Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome
since the 1997 annotation was published. The data presented here should be useful for analysis of
E. coli gene products as well as gene products encoded by other genomes.
Description
Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
Suggested Citation
Article: Serres, Margrethe H., Gopal, Shuba, Nahum, Laila A., Liang, Ping, Gaasterland, Terry, Riley, Monica, "A functional update of the Escherichia coli K-12 genome", Genome Biology 2 (2001): research0035.1–0035.7, DOI:10.1186/gb-2001-2-9-research0035, https://hdl.handle.net/1912/106Related items
Showing items related by title, author, creator and subject.
-
Rate zonal density gradient ultracentrifugation analysis of repair of radiation damage to the folded chromosome of Escherichia coli
Ulmer, Kevin M. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1978-04)The structure of the membrane-free nucleoid of Escherichia coli and of unfolded chromosomal DNA was investigated by sedimentation on neutral sucrose gradients after irradiation with 60Co gamma-rays and ultraviolet light ... -
Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12
Vo, Jason; Inwood, William; Hayes, John M.; Kustu, Sydney (2013-03-25)Organisms that use ammonium as the sole nitrogen source discriminate between [15N] and [14N] ammonium. This selectivity leaves an isotopic signature in their biomass that depends on the external concentration of ammonium. ... -
Extending knowledge of Escherichia coli metabolism by modeling and experiment
Voit, Eberhard O.; Riley, Monica (BioMed Central, 2003-10-28)One of the challenges for ‘post-genomic’ biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and ...