The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Caspi, Ron; Altman, Tomer; Billington, Richard; Dreher, Kate; Foerster, Hartmut; Fulcher, Carol A.; Holland, Timothy A.; Keseler, Ingrid M.; Kothari, Anamika; Kubo, Aya; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Ong, Quang; Paley, Suzanne; Subhraveti, Pallavi; Weaver, Daniel S.; Weerasinghe, Deepika; Zhang, Peifen; Karp, Peter D.

doi:10.1093/nar/gkt1103

Title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Journal Article · Tue Nov 12 00:00:00 EST 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt1103· OSTI ID:1904530

Caspi, Ron ^[1]; Altman, Tomer ^[1]; Billington, Richard ^[1]; Dreher, Kate ^[2]; Foerster, Hartmut ^[3]; Fulcher, Carol A. ^[1]; Holland, Timothy A. ^[1]; Keseler, Ingrid M. ^[1]; Kothari, Anamika ^[1]; Kubo, Aya ^[1]; Krummenacker, Markus ^[1]; Latendresse, Mario ^[1]; Mueller, Lukas A. ^[3]; Ong, Quang ^[1]; Paley, Suzanne ^[1]; Subhraveti, Pallavi ^[1]; Weaver, Daniel S. ^[1]; Weerasinghe, Deepika ^[1]; Zhang, Peifen ^[2]; Karp, Peter D. ^[1]

SRI International, Menlo Park, CA (United States)
Carnegie Institute of Science, Stanford, CA (United States)
Boyce Thompson Institute for Plant Research, Ithaca, NY (United States)

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

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Research Organization:: SRI International, Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: SC0004878; GM080746; GM077678; GM088849; GM75742; IOS-1026003; DBI-0640769

OSTI ID:: 1904530

Journal Information:: Nucleic Acids Research, Vol. 42, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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BioModels: ten-year anniversary Chelliah, Vijayalakshmi; Juty, Nick; Ajmera, Ishan Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1181	journal	November 2014
The Transporter Classification Database (TCDB): recent advances Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1103	journal	November 2015
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more Liu, Yifeng; Liang, Yongjie; Wishart, David Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv383	journal	April 2015
The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity Taxis, Tasia M.; Wolff, Sara; Gregg, Sarah J. Nucleic Acids Research https://doi.org/10.1093/nar/gkv973	journal	September 2015
Pathview Web: user friendly pathway visualization and data integration Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx372	journal	May 2017
Confronting the catalytic dark matter encoded by sequenced genomes Ellens, Kenneth W.; Christian, Nils; Singh, Charandeep Nucleic Acids Research, Vol. 45, Issue 20 https://doi.org/10.1093/nar/gkx937	journal	October 2017
Revisiting Demand Rules for Gene Regulation Prajapat, Mahendra Kumar; Jain, Kirti; Choudhury, Debika Molecular BioSystems https://doi.org/10.1101/014142	journal	January 2015
Detection of pathways affected by positive selection in primate lineages ancestral to humans Daub, J. T.; Moretti, S.; Davidov, I. I. Oxford Academic https://doi.org/10.1101/044941	journal	November 2016
Model-driven design of a minimal medium forAkkermansia muciniphilaconfirms mucus adaptation van der Ark, Kees C. H.; Aalvink, Steven; Suarez-Diez, Maria Microbial Biotechnology, Vol. 11, Issue 3 https://doi.org/10.1111/1751-7915.13033	journal	January 2018
Draft Genome Sequence of Olsenella scatoligenes SK9K4 ^T , a Producer of 3-Methylindole (Skatole) and 4-Methylphenol ( p -Cresol), Isolated from Pig Feces Li, Xiaoqiong; Højberg, Ole; Noel, Samantha Joan Genome Announcements, Vol. 4, Issue 1 https://doi.org/10.1128/genomea.00042-16	journal	February 2016
Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric Genome Announcements, Vol. 4, Issue 3 https://doi.org/10.1128/genomea.00608-16	journal	June 2016
Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium Gkorezis, Panagiotis; Bottos, Eric M.; Van Hamme, Jonathan D. Genome Announcements, Vol. 3, Issue 6 https://doi.org/10.1128/genomea.01517-15	journal	December 2015
Identification of Staphylococcus aureus Factors Required for Pathogenicity and Growth in Human Blood Connolly, John; Boldock, Emma; Prince, Lynne R. Infection and Immunity, Vol. 85, Issue 11 https://doi.org/10.1128/iai.00337-17	journal	November 2017
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment Hsu, Tiffany; Joice, Regina; Vallarino, Jose mSystems, Vol. 1, Issue 3 https://doi.org/10.1128/msystems.00018-16	journal	June 2016
Computational Approaches for Microalgal Biofuel Optimization: A Review Koussa, Joseph; Chaiboonchoe, Amphun; Salehi-Ashtiani, Kourosh BioMed Research International, Vol. 2014 https://doi.org/10.1155/2014/649453	journal	January 2014
Computational Identification of Metabolic Pathways ofPlasmodium falciparumusing thek-Shortest Path Algorithm Oyelade, Jelili; Isewon, Itunuoluwa; Aromolaran, Olufemi International Journal of Genomics, Vol. 2019 https://doi.org/10.1155/2019/1750291	journal	October 2019
Assessment of genome annotation using gene function similarity within the gene neighborhood Jun, Se-Ran; Nookaew, Intawat; Hauser, Loren BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1761-2	journal	July 2017
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA García-Romero, Inmaculada; Pérez-Pulido, Antonio J.; González-Flores, Yolanda Elisabet BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2411-1	journal	February 2016
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize Walsh, Jesse R.; Schaeffer, Mary L.; Zhang, Peifen BMC Systems Biology, Vol. 10, Issue 1 https://doi.org/10.1186/s12918-016-0369-x	journal	November 2016
Ascaris lumbricoides β carbonic anhydrase: a potential target enzyme for treatment of ascariasis Zolfaghari Emameh, Reza; Kuuslahti, Marianne; Vullo, Daniela Parasites & Vectors, Vol. 8, Issue 1 https://doi.org/10.1186/s13071-015-1098-5	journal	September 2015
Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J. Antonio BMC Research Notes, Vol. 8, Issue 1 https://doi.org/10.1186/s13104-015-1285-7	journal	August 2015
Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection Bello-Ortí, Bernardo; Howell, Kate J.; Tucker, Alexander W. Veterinary Research, Vol. 46, Issue 1 https://doi.org/10.1186/s13567-015-0225-9	journal	September 2015
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/s40793-015-0077-y	journal	October 2015
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru Microbes and Environments, Vol. 31, Issue 3 https://doi.org/10.1264/jsme2.me16024	journal	January 2016
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0 Granger, Brian R.; Chang, Yi-Chien; Wang, Yan PLOS Computational Biology, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pcbi.1004875	journal	April 2016
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas PLOS Computational Biology, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pcbi.1005252	journal	December 2016
Phenotypic Profiling of Scedosporium aurantiacum, an Opportunistic Pathogen Colonizing Human Lungs Kaur, Jashanpreet; Duan, Shu Yao; Vaas, Lea A. I. PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0122354	journal	March 2015
The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells Murayama, Satohiko; Ishikawa, Shu; Chumsakul, Onuma PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0131588	journal	July 2015
Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature Penesyan, Anahit; Kumar, Sheemal S.; Kamath, Karthik PLOS ONE, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pone.0138527	journal	October 2015
Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach Arfken, Ann; Song, Bongkeun; Bowman, Jeff S. PLOS ONE, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pone.0185071	journal	September 2017
Tools for visualization and analysis of molecular networks, pathways, and -omics data Habermann, Bianca; Villaveces, Jose; Koti, Prasanna Advances and Applications in Bioinformatics and Chemistry https://doi.org/10.2147/aabc.s63534	journal	June 2015
Identification of novel drug targets in bovine respiratory disease: an essential step in applying biotechnologic techniques to develop more effective therapeutic treatments Sakharkar, Meena; Rajamanickam, Karthic; Chandra, Ramesh Drug Design, Development and Therapy, Vol. Volume 12 https://doi.org/10.2147/dddt.s163476	journal	May 2018
Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan Frontiers in Bioengineering and Biotechnology, Vol. 2 https://doi.org/10.3389/fbioe.2014.00066	journal	December 2014
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments Dziewit, Lukasz; Bartosik, Dariusz Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00596	journal	November 2014
Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals Dziewit, Lukasz; Pyzik, Adam; Szuplewska, Magdalena Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00152	journal	March 2015
Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3 Rivers, Adam R.; Burns, Andrew S.; Chan, Leong-Keat Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00380	journal	March 2016
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems Cai, Mingwei; Wilkins, David; Chen, Jiapeng Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00778	journal	May 2016
“Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants Albertsen, Mads; McIlroy, Simon J.; Stokholm-Bjerregaard, Mikkel Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01033	journal	July 2016
The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor Brumm, Phillip J.; Gowda, Krishne; Robb, Frank T. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01979	journal	December 2016
Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion Bonifay, Vincent; Wawrik, Boris; Sunner, Jan Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00099	journal	January 2017
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation Mendoza, Sebastián N.; Cañón, Pablo M.; Contreras, Ángela Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00534	journal	March 2017
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling Triana, Sergio; de Cock, Hans; Ohm, Robin A. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01772	journal	September 2017
Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149 Tkavc, Rok; Matrosova, Vera Y.; Grichenko, Olga E. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02528	journal	January 2018
Network Analyses in Plant Pathogens Botero, David; Alvarado, Camilo; Bernal, Adriana Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00035	journal	January 2018
Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake Vigneron, Adrien; Lovejoy, Connie; Cruaud, Perrine Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01656	journal	July 2019
VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera) Naithani, Sushma; Raja, Rajani; Waddell, Elijah N. Frontiers in Plant Science, Vol. 5 https://doi.org/10.3389/fpls.2014.00644	journal	December 2014
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations Gopalakrishnan, Saratram; Maranas, Costas Metabolites, Vol. 5, Issue 3 https://doi.org/10.3390/metabo5030521	journal	September 2015
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics Rai, Aswathy N.; Epperson, William B.; Nanduri, Bindu Bioinformatics and Biology Insights, Vol. 9s2 https://doi.org/10.4137/bbi.s30525	journal	January 2015
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products Esch, Robert; Merkl, Rainer Universität Regensburg https://doi.org/10.5283/epub.44220	text	January 2020
Identification of potential drug targets and vaccine candidates in Clostridium botulinum using subtractive genomics approach Sudha, Rati; Katiyar, Amit Bioinformation, Vol. 15, Issue 1 https://doi.org/10.6026/97320630015018	journal	January 2019
The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization Nelson, David R.; Khraiwesh, Basel; Fu, Weiqi eLife, Vol. 6 https://doi.org/10.7554/elife.25783	journal	June 2017

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