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The Profiling of Escherichia coli chromosome (PEC) database has been constructed to compile any
relevant information that could help to characterize the E. coli genome, especially with respect
to discovering the function of each gene. The database is intended to provide an interface comprehensible
to most experimental researchers. The E. coli genetic resource committee of Japan supports the
construction and maintenance of this database.
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The following information is available from PEC.
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Information is available from PEC
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| (1) |
Basic information about each gene (gene name, direction, length, location, etc.) |
| (2) |
The essentiality of each gene for cell growth, classified as essential, non-essential, or unknown
based on information from research reports and deletion mutation studies.
The criteria for classification are described below (*1).
References, on which the classification is based, are listed in the format "Medline (PMID)" in
the section for each gene
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| (3) |
The names of the strains related to each gene, which are stored in the Stock center of the Natl.
Inst. Genet, Japan.
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| (4) |
Results of similarity searches for each gene product (BLAST, PSI-BLAST, FASTA) |
| (5) |
Structural features (domain, motif, etc.) for each gene product |
| (6) |
Results of comparative analyses of each gene (homologous in other sequenced bacteria, etc.). |
| (7) |
Information from rather long deletion mutations. |
| (8) |
Locations of Kohara clones. |
PEC provides the following overviews.
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overview
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Explanation
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| Circular |
The E. coli genome is displayed as a circle, on which the locations of the tRNA genes have been
marked. Essential genes, non-essential genes, and unknown genes are painted in different colors,
allowing easy visualization of their distribution on the genome.
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| Linear |
The E. coli genome is linearly displayed. Each gene is displayed in a linear manner along the
genome together with its name, direction, size, location, and class (essential, non-essential,
unknown). Also, the regions deleted in the deletion mutant(s) for each gene are shown. This view
also shows classical markers, whose exact locations remain unknown, contig information, and the
location of the Kohara clones. As the Kohara clones are derived from the strain W3110, their positions
were assigned by doing a homology search on the MG1655 genome.
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| Motif |
Structural domains and motifs of a gene product are displayed graphically along with those of
other genes having the same domains or motifs.
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PEC is based on the sequence information of E. coli strain MG1655. Information, such as basic information
(gene name, direction, length, location, etc.) about each gene, was retrieved from the other databases
listed below (*2) and annotated before incorporation
into the PEC database.
We appreciate any comments on how to improve the database.
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yyamazak[at]lab.nig.ac.jp (
database construction ) |
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jkato[at]comp.metro-u.ac.jp ( research
activity ) |
(*1) Gene classification based on essentiality
for cell growth
All of the E. coli genes were classified into three groups, (1) genes essential for cell growth
(essential), (2) those dispensable for cell growth (non-essential),
and (3) those unknown to be essential or non-essential, mainly
using information taken from journal articles and the following criteria.
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Reference
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Explanation
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A:
experimental evidence known |
Basically, when a strain having only a null type mutation in a gene (without other suppressor
mutations) was able to grow, even if the mutation meant that the strain could grow only at a certain
temperature or under certain nutrient conditions, it is classified into the "non-essential" category. |
| (1) The genes, for which null type mutants (having deletion or Tn (transposon)
insertion mutations) have been isolated, are classified into the "non-essential" category. |
| (2) The genes located within the deleted regions of identified deletion
mutations are classified into the "non-essential" category. |
| (3) The genes that do not fall under (1) or (2) and for
which conditional lethal mutants have been isolated, are classified into the "essential" category. |
B:
no experimental evidence known |
The genes described below are classified as follows without any experimental
evidences. |
| (4) The structural genes of ribosomal proteins are classified into the "essential" category
except for those that have been reported to be dispensable. |
| (5)The argX, cysT, glyT, hisR, leuU, leuW, leuZ, proL, proM, serT, serV,
thrU, trpT genes coding for unique tRNAs are classified into the "essential" category. |
| (6) The hisS and argS genes coding for unique aminoacyl tRNA synthases
are classified into the "essential" category. |
| (7) The genes involved in flagellation, motility, and chemotaxis (flg,
flh, fli, mot, che, tap, tar) are classified into the "non-essential" category. |
| (8) The hem genes, whose mutants can grow when porphyrin is added to
the culture media, are classified into the "non-essential" category. |
C:
others |
The genes, which do not correspond to those listed in A and B, are classified
into the "unknown" category. |
(*2) References:
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References
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Link
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| Essential Gene & Minimal Genome, Deletions |
"Cell Size and Nucleoid Organization of Engineered Escherichia coli Cells with a Reduced Genome."
Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K, Ote T, Yamakawa T, Yamazaki Y, Mori H, Katayama T, Kato J.
Molecular Biology (2005) 55(1), 137-149.
"Construction of consecutive deletions of the Escherichia coli chromosome"
Jun-ichi Kato and Masayuki Hashimoto
Mol Syst Biol. 2007; 3: 132.
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| Sequence Data |
U00096.2 26-FEB-2013
(http://www.ncbi.nlm.nih.gov/nuccore/U00096.2)
AE000111-AE000510, last updated in 1998
(http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&gi=115 )
Frederick R. Blattner et al., University of Wisconsin-Madison, USA
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| Linkage map of E. coli K-12, Edition 10: The traditional map |
(PubMed)
Mary K. B. Berlyn, Yale University, USA
Microbiol. Mol. Biol. Rev., 62,814-984, 1998 |
| "E. coli database collection" (ECDC) |
(http://www.uni-giessen.de/~gx1052/ECDC/ecdc.htm)
Justus-Liebig-University, Germany |
| "Verified Protein Starts" |
(http://www.ecogene.org/3.0/?q=ecodownload)
Data compiled from the literature and the appropriate citations are available from EcoGene. |
| "Completing the E.coli Proteome" |
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10705439&dopt=Abstract)
Dr. Gavin H. Thomas,
Department of Molecular Biology and Biotechnology,
University of Sheffield |
| "Operon" |
(http://regulondb.ccg.unam.mx/data/OperonSet.txt)
Data sets of the RegulonDB database |
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About PEC (Tours)
