Heme, Not Just the Red Pigment in Blood.

Heme, an iron-containing porphyrin, functions as a prosthetic group in numerous proteins. These range from components of the electron transport chain to many enzymes. No wonder the biosynthesis of heme is highly conserved in evolution!

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Scanning Electron Microscope Image of Blood Cells

Scanning Electron Microscope Image of Blood Cells, put in the public domain by NCI/Donald BlissBruce Wetzel and Harry Schaefer.

Navigate Metabolic Map for Pathways

The Cellular Overview enables you to browse through a zoomable metabolic map diagram that displays pathways according to groups based on biological function, or classes of metabolites produced/consumed.

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a portion of a Cellular Overview diagram,
				showing several pathway classes

Cellular overview image generated by Pathway Tools

Important Mammalian Pathways: The Urea Cycle

The urea cycle is responsible for mediating excretion of nitrogenous waste. It was the first metabolic pathway to be discovered, five years before the discovery of the TCA cycle. The cycle occurs across both the cytosol and the mitchondrion.

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colorized electron micrograph of mitochondria in
			    a mammalian lung cell

colorized selection from Mitochondria, mammalian lung - TEMput in the Public Domain by author, Louisa Howard.

RouteSearch: Search for Paths through the Metabolic Network

Search for lowest-cost paths through the metabolic network of the selected organism. Or, design lowest-cost pathways to novel compounds by adding reactions from MetaCyc.

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a schematic showing 3 hypothetical
				    routes from one compound to another, one
				    that is very long, one that is short but
				    most of the atoms from the starting compound
				    do not end up in the target compound, and
				    the best route, which is intermediate in
				    length but conserves the atoms in the
				    starting compound.


A Pathway Linked to Central Nervous System Disorders

The GABA shunt forms a closed loop in the CNS for conserving the supply of the excitatory neurotransmitter GABA. One of the enzymes of this pathway, 4-aminobutyrate aminotransferase is a target for the anti-epileptic drug vigabatrin.

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Brain MRI

selection from Brain MRI Source: Dr. Leon Kaufman. UCSF.

Metabolomics Data Analysis

Multiple tools are available in this website for metabolomics data analysis.

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Enrichment dialog displayed over SmartTable

SmartTable display generated by Pathway Tools.

The Truth about the Thanksgiving Turkey...

Of the 20 amino acids, at least 9 are essential. Essential L-tryptophan is required for serotonin, melatonin and niacin synthesis. Its requirement for NAD biosynthesis was discovered when humans stricken with pellagra recovered after the addition of tryptophan or niacin to their diets.

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Gene Expression Data Analysis

Multiple tools are available in this website for analysis of gene expression data.

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a portion of a cellular overview diagram,
					 overlaid with a gene expression time series
					 dataset. Detail popups are shown for three
					 reactions in three different styles: a bar
					 chart, a heatmap, and a line graph.

Cellular Overview Omics Viewer image generated by Pathway Tools.

HumanCyc: Encyclopedia of Human Genes and Metabolism

HumanCyc provides an encyclopedic reference on human metabolic pathways, the human genome, and human metabolites.

HumanCyc is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button above to explore the available databases.

For more information on HumanCyc, see our article "Computational prediction of human metabolic pathways from the complete human genome" in Genome Biology.

User Guide

What people are saying

"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 Series

Tutorial #1: Introduction to BioCyc
These six sequential segments, giving you a guided tour of the BioCyc collection in concise bites. To download or view, just click on one of the links following each segment's name.
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.