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Plant Metabolic Pathways

The pathways section in the Gramene databases is home for RiceCyc, MaizeCyc, BrachyCyc and SorghumCyc, the pathway databases for rice, maize, Bracypodium, and sorghum, respectively. It also provides mirrors of pathway databases from Arabidopsis, tomato, potato, pepper, coffee, Medicago, E. coli, and the MetaCyc and PlantCyc reference databases, and might enable comparative analysis again upon software upgrade that supports the most current version of ptools software 17.0 by the original sources, such as the SolGenomics Network (SGN). In addition to search and browse functions, the database allows users to find genes mapped to respective reactions and pathways and draw inetrspecific comparison between the pathways.

Pathways Browse and Other Options

Click on the species specific links such as browse to go through the list of pathways; summary to get a summarized overview. Click on the more info link to learn more details on the respective pathway database.

RiceCyc ver 3.3 
Oryza sativa japonica

Strain: Nipponbare
Browse | SummaryMore info
AraCyc* ver 10.0 
Arabidopsis thaliana
Strain: Columbia
Browse | SummaryMore info
EcoCyc* ver 17.0  
Escherichia coli
Strain: K-12 MG1655
Browse | SummaryMore info

SorghumCyc ver 1.1  
Sorghum bicolor
Strain: BTx623
Browse | SummaryMore info

MedicCyc* ver 1.0.1 
Medicago truncatula, Barrelclover
Browse | SummaryMore info

MetaCyc* ver 17.0 
Reference Pathway Database
Strain: not applicable
Browse | SummaryMore info

MaizeCyc ver 2.1 
Zea mays
Strain: B73
Browse | SummaryMore info

PoplarCyc* ver 5.0 
Populus trichocarpa (and other Populus species and hybrids)
Strain: n/a
Browse | SummaryMore info

PlantCyc* ver 7.0 
Plant Metabolic Pathway Database
Strain: not applicable
Browse | SummaryMore info

BrachyCyc ver 2.0 
Brachypodium distachyon
Strain: Bd21
Browse | SummaryMore info

PotatoCyc* ver 1.0.1 
Solanum tuberosum, Potato
Strain: n/a
Browse | SummaryMore info

CoffeaCyc* ver 1.1.1 
Coffea canephora, Coffee
Strain: n/a
Browse | SummaryMore info

LycoCyc* ver 2.0.1 
Solanum lycopersicum, Tomato
Strain: n/a
Browse | SummaryMore info

* Mirror database. Not curated by the Gramene database. Click on more info link for details.

Other Tools

Omics Viewer: Upload and view the realtime mappings of your datasets from microrray expression, proteomics, metabolomics on Pathway overview diagram
Comparative analysis: Compare data sets from two or more species for reactions, pathways, compounds, proteins, transporters and/or transcription units


Help Presents an overview on how to use the pathway database and lists explanations of field names.
Tutorial More in-depth than the help pages, use the tutorial for an example of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Release Notes For more information about the most recent release.

Quicklink for selected rice pathways

Auxin metabolism
Brassinosteroid metabolsm
Cytokinin metabolism
Ethylene biosynthesis from methionine
Gibberellin metabolism
Jasmonic acid biosynthesis
Salicylic acid biosynthesis
Pentose phosphate pathways
Secondary metabolic pathways
Starch biosynthesis
TCA cycle

ALL pathways


Useful external links

KEGG pathways
KEGG rice pathways
IUBMB Enzyme nomenclature
Brenda enzyme database
ENZYME at Expasy
Cellular Expression Profiling of Rice
Rice oligonucleotide array project