Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.

BsubCyc Overview

BsubCyc is a model-organism database for the bacterium Bacillus subtilis and is based on the updated B. subtilis 168 genome sequence and annotation published by Barbe et al. in 2009. Gene function annotations are being updated when new literature is available.

Getting Started

New to BsubCyc? Explore the database!

    Retrieve the sequence of your favorite gene: Finding the sequence for your favorite gene is simple. Type the gene name into the "Quick Search" box at the top right of this page. Click on "Gene Search", which will bring you directly to the gene page unless the gene name is ambiguous. In the "Operations" menu on the right side, click on the "Nucleotide Sequence" link to retrieve the sequence from the start to the stop codon, with an option to add additional upstream and downstream sequence e.g. for primer design.

    Clickable links: Many of the items shown on a gene/protein/pathway page are clickable and lead you to more information about this database object. Give it a try!

User Guide >>
  • Regulatory Overview

    Regulatory Overview image generated by Pathway Tools

    Browse the Regulatory Connections Between Genes

    The Regulatory Overview enables you to browse through the regulatory network of B. subtilis and overlay experimental data such as gene expression values.

    Try it Now >>
  • Cellular Overview

    Cellular Overview image generated by Pathway Tools

    Browse the Metabolic Network of B. subtilis

    The Cellular Overview enables you to browse through the metabolic network of B. subtilis. Search for your favorite enzyme or metabolite and find out where it fits in the big picture.

    Try it Now >>
  • Genome Browser

    Genome Browser image generated by Pathway Tools

    Browse the Bacillus subtilis Genome

    Search for your favorite gene in the Genome Browser and learn about its neighbors in the genome.

    Try it Now >>
  • SmartTables

    SmartTable example

    Create and Manage Lists of Things With SmartTables

    SmartTables allow you to generate, analyze and transform lists of objects (genes, enzymes, pathways and more).

    Learn More

Tools

BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:

New in BsubCyc

We have added protein features from the UniProt database to proteins in BsubCyc. In addition, we have added links to the Bacillus Genetic Stock Center from the gene/protein pages of many of the genes for which null mutant strains are available at the BGSC.

Older updates to BsubCyc are archived here. The full BsubCyc release history is available here.

How to Cite BsubCyc

Please cite BsubCyc as Caspi et al. (2014), “The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases”, Nucleic Acids Research 42:D459-D471.

Video Tutorials

The BioCyc Video series introduces users to the basic and advanced features of the BioCyc website and the Pathway Tools software. A complete list of videos in additional download formats are available on the Video and Podcast page.

This video introduces the BioCyc.org site and the BioCyc collection of hundreds of Pathway/Genome Databases and covers:

  • BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
  • How to search, browse, and find what you need in the BioCyc collection
  • How we represent metabolism, transcription, and all their parts