EcoCyc

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EcoCyc
Who:	Peter Karp, SRI
What:	Comprehensive database of E. coli' molecular components
Where:	EcoCyc
Updates	Every 3 months
Upcoming events	link to event calendar, if applicable
Web Services

About EcoCyc

EcoCyc is a database of literature-based "gold standard" annotation of the molecular components of E. coli K-12, primarily referencing strain MG1655. EcoCyc is a central part of the BioCyc collection of database at SRI International in Menlo Park, CA.

Content

Genes, Proteins, Compounds, and everything related. All possible types of pathways

Reactions:

 Binding 
 DNA repair
 EC 
 Protein-Ligand
 Reactions of Two Component Regulators
 Transport Reactions 
 Unclassified Reaction

Any possible type of Compound

Metabolic chart

 you can actually paint omics data onto the diagram

Omics Viewer

Using EcoCyc

Searching

When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also referenced, with the bibliography at the bottom of the linked page.
query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

Usage examples

Add links to additional pages describing success stories here.

Input: parC Initial Output: Choice between the Gene, or the Protein product

If gene is selected, the output yields: Synonyms Superclasses GO (gene ontology) terms Map Position Sequence Length Products Reaction Schematic (the only thing I see that this does is link to the protein page) Unification Links (identifiers of parC in other databases) Ortholog Links Alignment Tool Genomic Location w.r.t. Direction and Flanking Genes

If the protein link is selected, the output yields: Synonyms Comments about quaternary structure in solution Gene Cellular Location Subunit Composition Length MW Component of (what enzyme the protein is a subunit of) Unification Links Relationship Links Comments about Topo IV with all relative references Bibliography

Discussion

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References

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp. EcoCyc: A comprehensive database resource for Escherichia coli, Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L., Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J., The comprehensive updated regulatory network of Escherichia coli K-12 BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr., The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database ASM News 70(1):25-30 2004.

External Links

EcoCyc