MetaCyc

Ajmaline is an antiarrhythmic agent produced by the plant Rauvolfia serpentina. Why is it named after the Indian physician Hakim Ajmal Khan?

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[画像:Rauvolfia serpentina, a plant with red stems and blue-black berries]

A cropped version of the image Chandra by Dinesh Valke. Used under creative commons license.

Can the enzyme oxalate oxidase (EC 1.2.3.4) save the American chestnut? Yes, if you ask Darling 58.

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Saffron is arguably the most expensive spice in the world. But what does it have to do with Covid-19?

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[画像:Purple saffron flowers]

Autumn crocus! by Sylvia Sassen. Used under creative commons license.

The Bible tells us that the ancient Israelites were fed manna that fell from the sky while crossing the Sinai desert. But what is manna?

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Why did Cleopatra, the queen of Egypt, dilate her pupils to look larger? Well, we can't tell you why, but we can tell you how.

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[画像:Cleopatra holding black cat Bastet]

Granted Audience with Cleopatra and Bastet by Stella Splendid. Used under Creative Commons license.

Have you ever swum in the ocean and started to itch? Care to know why?

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[画像:Man lying on surfboard in the ocean]

Coral Reef, taken by Susan Hazlett, USGS.Public domain.

How long can mammals live without oxygen? Find out!

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[画像:Whimsical drawing of a naked mole rat]

IMG_20161015_161456 by Julie Freeman. Used under Creative Commons license

Vanillin goes with desserts. Chilli peppers go with salsa. But you can't have salsa without vanillin.

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[画像:row of chili peppers]

Chili pepper by hepp. Used under creative commons license

Chitin is the second most common polymer in the world, after cellulose. Our understanding of its degradation was significantly boosted with the discovery of LPMOs. And what are LPMOs?

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What do bile acids have to do with a bear? And why you should be aware?

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[画像:Polar bear in water]

Polar bear by Leszek.Leszczynski. Used under creative commons license.

MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life.

MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.

MetaCyc currently contains 3,153 pathways, 19,020 reactions and 19,372 metabolites.

MetaCyc applications include:

  • Online encyclopedia of metabolism
  • Predict metabolic pathways in sequenced genomes
  • Support metabolic engineering via enzyme database
  • Metabolite database aids metabolomics research

Guide To MetaCyc

What people are saying
See more BioCyc testimonials

"BsubCyc is a tool of the utmost value."

Penn State

Paul Babitzke
Prof. of Biochemistry
& Molecular Biology

"My lab uses these resources on a daily basis."

University of Wisconsin

Patricia Kiley,
Professor and Chair,
Dep't. of Biomolecular Chemistry

"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."

University of Minnesota

Arkady Khodursky
Assoc. Prof. Biochemistry

"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."

Pacific Northwest National Lab

William Cannon, Team Lead
Computational Biology

"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."

Ginkgo Bioworks

"BioCyc is a tremendous resource for pathway analysis in metabolomics."

University of Georgia

Art Edison, Dept of Genetics

"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."

Great Lakes Bioenergy

Timothy J. Donohue, Director

"I have not found another database that has a better interface than BioCyc."

University of Michigan

Gary B. Huffnagle, Professor
Microbiology and Immunology

Learning Library

Tutorial Videos

Tutorial #1: Introduction to BioCyc
Tutorial #2: Introduction to SmartTables
The following Tutorial will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below.
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
Tutorial #4: Omics Data Analysis
This tutorial will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Tutorial #5: Pathway Collages
Pathway collages are multi-pathway diagrams that you can customize by, for example, overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. Learn how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways.
Tutorial #6: Creating a Pathway/Genome Database
Tutorial #7: Using the Structured Advanced Query Page
An introduction to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. You'll learn about:The basic steps of setting up an advanced query; Four examples of increasingly complex queries, including how to query across multiple databases; Where to learn more about the structure of BioCyc databases.