List of BioCyc Pathway/Genome Databases

The 20,078 databases within the BioCyc collection as of December 10, 2024 (version 28.5) are as follows.

Click here to request the addition of a Tier 3 PGDB for a new genome to BioCyc.

The EcoCyc database is freely available to all users because its curation is supported by NIH funding. Also free is the database for the cyanobacterium Arthrospira platensis NIES-39 as an example of a Tier 3 database. The other BioCyc databases are available via subscription, which supports their curation.

Tier 1 Databases

PGDBs in Tier 1 have received at least one year of literature-based curation by scientists. For example, the EcoCyc DB is the result of more than 20 person-years of effort to enter information from the E. coli literature about the metabolism, transport, and genetic regulatory processes of this organism, and to update the genome annotation to reflect newly characterized E. coli genes.

Database	Contents	Organization	URL
MetaCyc	Metabolic pathways and enzymes from multiple organisms	SRI International	metacyc.org
EcoCyc	Escherichia coli K-12 substr.MG1655	SRI International, Macquarie University, National University of Mexico	ecocyc.org
HumanCyc	Homo sapiens	SRI International	humancyc.org
AraCyc	Arabidopsis thaliana	S. Rhee,Department of Plant Biology, Carnegie Institution	aracyc
YeastCyc	Saccharomyces cerevisiae	SRI International, SGD Curators, Stanford University	yeast.biocyc.org

Tier 2 Databases

PGDBs in Tier 2 were generated by the PathoLogic program, which was used to predict their metabolic pathways, their operons (for bacteria only), and their pathway hole fillers (for many of the PGDBs). The resulting PGDBs underwent manual review and curation to remove false-positive pathway predictions, add new protein functions and metabolic pathways from the literature, create protein complexes, and connect enzymes with reactions they catalyze. In some cases external datasets (e.g., gene essentiality data) have been loaded into these PGDBs. Most Tier 2 PGDBs have undergone 1-4 months of curation.

Click on the name of a database to navigate to the home page for that database for more information, such as the database authors, and statistics on the database content.

Database	Organization
Acinetobacter baumannii AB5075	Macquarie University, SRI International
Acinetobacter baumannii ATCC 17978	Macquarie University, SRI International
Agrobacterium fabrum C58	SRI International
Alteromonas macleodii ATCC 27126	SRI International; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Ben-Gurion University of the Negev, Hebrew University of Jerusalem, Macquarie University; University of Alabama, Birmingham; University of California, San Diego; University of Haifa, University of Natural Resources and Life Sciences, University of North Carolina, Chapel Hill
Anopheles gambiae	Ezekiel Adebiyi, Olubanke Ogunlana, Covenant University
Aurantimonas manganoxydans SI85-9A1	SRI International
Bacillus anthracis Ames	SRI International
Bacillus subtilis subtilis 168	SRI International, Macquarie University
Bifidobacterium longum longum JCM 1217
Brucella abortus 2308	Macquarie University, SRI International
Brucella ovis ATCC 25840	SRI International, Macquarie University
Candida albicans SC5314	Candida Genome Database, Stanford University
Candidatus Cardinium hertigii	Cavanilles Institute of Biodiversity and Evolutionary Biology
Candidatus Evansia muelleri	Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Bayreuth
Candidatus Portiera aleyrodidarum BT-QVLC	Cavanilles Institute of Biodiversity and Evolutionary Biology
Caulobacter crescentus NA1000	Stanford University, SRI International
Caulobacter vibrioides CB15	SRI International, Stanford University
Chlamydia trachomatis D/UW-3/CX	Macquarie University, SRI International
Clostridioides difficile 630	SRI International, Macquarie University, University of Iowa
Clostridioides difficile R20291	Macquarie University, University of Iowa
Clostridium saccharoperbutylacetonicum N1-4HMT	SRI International
Collinsella aerofaciens ATCC 25986	SRI International
Corynebacterium glutamicum ATCC 13032	SRI International
Desulfovibrio piger ATCC 29098	SRI International
Drosophila melanogaster	Kenneth L Wiley, Harvard University
Enterococcus faecalis V583
Enterococcus faecalis OG1RF
Escherichia coli B str. REL606	SRI International
Escherichia coli CFT073	SRI International
Escherichia coli K-12 substr. W3110	SRI International
Escherichia coli O157:H7 str. EDL933	SRI International
Faecalibacterium prausnitzii A2-165	SRI International
Helicobacter pylori 26695	SRI International, Macquarie University
Klebsiella pneumoniae NTUH-K2044	SRI International, Macquarie University
Lactobacillus plantarum WCFS1	Macquarie University, SRI International
Lactobacillus rhamnosus GG	SRI International
Lactococcus lactis lactis IL1403	Macquarie University, SRI International
Leishmania major strain Friedlin	Bio21 Molecular Science and Biotechnology Institute, University of Melbourne SRI International
Listeria monocytogenes 10403S	Renato H. Orsi, Department of Food Science - Cornell University
Methanobrevibacter smithii ATCC 35061	SRI International
Methanocaldococcus jannaschii DSM 2661	Centre for Research and Technology Hellas (Greece), SRI International
Mus musculus	Jackson Laboratory
Mycobacterium tuberculosis CDC1551	SRI International
Mycobacterium tuberculosis H37Rv	SRI International, Macquarie University
Penicillium rubens Wisconsin 54-1255	Zheng Zhao, Delft University of Technology
Plasmodium falciparum 3D7	SRI International
Porphyromonas gingivalis W50	SRI International
Prevotella copri DSM 18205	SRI International
Prochlorococcus marinus marinus CCMP1375	SRI International, Macquarie University
Prochlorococcus marinus pastoris CCMP1986	SRI International, Macquarie University
Pseudomonas putida KT2440	SRI International
Salmonella enterica enterica serovar Typhimurium str. 14028S	SRI International
Salmonella enterica enterica serovar Typhimurium str. LT2	SRI International
Salmonella enterica enterica serovar Typhimurium str. SL1344	SRI International
Schistosoma mansoni	Adhemar Zerlotini Neto, FIOCRUZ
Shigella flexneri 2a str. 2457T	SRI International
Sinorhizobium meliloti 1021	SRI International
Staphylococcus aureus aureus NCTC 8325	SRI International, Macquarie University
Staphylococcus epidermidis RP62A	SRI International, Macquarie University
Streptococcus pneumoniae D39V	SRI International, Macquarie University
Streptomyces coelicolor A32	University of Warwick John Innes Centre
Sulfurospirillum multivorans	Department of Applied and Ecological Microbiology Research Group Medical Systems Biology
Synechococcus elongatus PCC 7942	SRI International
Synechococcus sp. WH 8102	Macquarie University, SRI International
Synechocystis sp. PCC 6803 substr. Kazusa	SRI International,Virginia Commonwealth University
Thalassiosira pseudonana CCMP1335	Karen Parker, Moss Landing Marine Labs
Trypanosoma brucei	French National Institute of Agricultural Reasearch (INRA), University of Glasgow (UoG)
Vibrio cholerae O1 biovar El Tor str. N16961	SRI International, Macquarie University
[Clostridium] symbiosum WAL-14163	SRI International
[Eubacterium rectale] ATCC 33656	SRI International

Tier 3 Databases

The 19,936 PGDBs in Tier 3 were generated by the PathoLogic program, which was used to predict their metabolic pathways and their operons (for bacteria only). The resulting PGDBs did not undergo manual review of the pathway predictions, nor subsequent literature curation. Therefore, the pathway predictions should be treated with due caution. PathoLogic is tuned to err on the side of over-predicting pathways to bring them to scientists' attention, rather than under-predicting pathways.

The Tier 3 DBs are available for adoption [more] by interested scientists, to undergo curation and updating.

Click on the name of a database to navigate to the home page for that database for more information, such as the database authors, and statistics on the database content.

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List of BioCyc Pathway/Genome Databases

Tier 1 Databases

Tier 2 Databases

Tier 3 Databases