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[[File:Database]]|thumb|Database]]]] {{Short description|Database of metabolic pathways and enzymes}}
[[File:Database.png|thumb]] {{DISPLAYTITLE:MetaCyc}}
{{Infobox database
| title = MetaCyc
| logo =
| description = Database of metabolic pathways and enzymes
| scope = Metabolic pathways, enzymes, and metabolic networks
| center = [[SRI International]]
| laboratory =
| author =
| released =
| url =
| download =
| webapp =
| sql =
| current_ref =
| versioning =
| license =
| frequency =
| curation =
}}


'''MetaCyc''' is a comprehensive [[database]] of [[metabolic pathways]] and [[enzymes]] from a wide variety of [[organisms]]. It is curated and maintained by [[SRI International]], a nonprofit scientific research institute. MetaCyc provides detailed information on metabolic pathways, enzymes, and the [[genes]] that encode them, making it a valuable resource for researchers in the fields of [[biochemistry]], [[molecular biology]], and [[systems biology]].
'''MetaCyc''' is a comprehensive [[metabolic pathway]] database that provides curated information on metabolic pathways and enzymes from all domains of life. It is a valuable resource for researchers in the fields of [[biochemistry]], [[molecular biology]], and [[systems biology]].


== Overview ==
==Overview==
MetaCyc contains curated data on metabolic pathways and enzymes from all domains of life, including [[bacteria]], [[archaea]], [[eukaryotes]], and [[viruses]]. The database includes information on the chemical reactions that occur within these pathways, the enzymes that catalyze these reactions, and the genes that encode these enzymes. MetaCyc also provides information on the [[metabolites]] involved in these pathways.
MetaCyc is designed to serve as a reference database for metabolic pathways and enzymes. It contains detailed information about individual pathways, including the reactions involved, the enzymes that catalyze these reactions, and the genes that encode these enzymes. MetaCyc is used for a variety of purposes, including the annotation of [[genomes]], the study of [[metabolic networks]], and the development of [[metabolic models]].


== Features ==
==History==
MetaCyc offers several features that make it a useful tool for researchers:
MetaCyc was originally developed as part of the [[EcoCyc]] project, which focused on the metabolism of ''[[Escherichia coli]]''. Over time, MetaCyc expanded to include pathways from a wide range of organisms, making it a universal resource for metabolic pathway information. The database is continuously updated and curated by experts in the field.
* **Pathway/Genome Databases (PGDBs)**: MetaCyc includes a collection of PGDBs that provide detailed information on the metabolic pathways and enzymes of specific organisms.
* **Pathway Tools Software**: MetaCyc is integrated with the Pathway Tools software, which allows users to visualize and analyze metabolic pathways and networks.
* **Comparative Analysis**: Researchers can use MetaCyc to compare metabolic pathways and enzymes across different organisms, helping to identify conserved and unique metabolic features.
* **Data Export**: Users can export data from MetaCyc in various formats for use in other applications and analyses.


== Applications ==
==Content==
MetaCyc contains information on over 2,500 metabolic pathways, 13,000 reactions, and 11,000 enzymes. The database includes pathways from [[bacteria]], [[archaea]], [[eukaryotes]], and [[plants]]. Each pathway entry in MetaCyc provides detailed information, including:
 
* A description of the pathway and its biological significance.
* The list of reactions that comprise the pathway.
* The enzymes that catalyze each reaction, along with their [[Enzyme Commission number|EC numbers]].
* The genes that encode the enzymes, when known.
* References to the scientific literature.
 
==Applications==
MetaCyc is used in a variety of research applications, including:
MetaCyc is used in a variety of research applications, including:
* **Metabolic Engineering**: Researchers use MetaCyc to design and optimize metabolic pathways for the production of biofuels, pharmaceuticals, and other valuable chemicals.
* **Systems Biology**: MetaCyc provides a comprehensive resource for modeling and analyzing metabolic networks, helping researchers understand the complex interactions within biological systems.
* **Comparative Genomics**: By comparing the metabolic pathways of different organisms, researchers can gain insights into the evolution of metabolism and identify potential targets for drug development.


== Related Databases ==
* '''Genome Annotation''': MetaCyc is used to annotate the metabolic pathways present in newly sequenced genomes.
MetaCyc is part of a larger family of databases that includes:
* '''Metabolic Engineering''': Researchers use MetaCyc to identify potential targets for metabolic engineering in order to optimize the production of desired compounds.
* [[BioCyc]]
* '''Systems Biology''': MetaCyc provides a framework for the construction of [[metabolic models]] that can be used to simulate and analyze metabolic networks.
 
==Access and Tools==
MetaCyc is freely accessible online and provides a variety of tools for users, including:
 
* '''Pathway Tools Software''': A suite of software tools for pathway analysis and visualization.
* '''BioCyc Database Collection''': A collection of organism-specific databases that are derived from MetaCyc.
* '''Web Services''': APIs that allow programmatic access to MetaCyc data.
 
==Also see==
* [[EcoCyc]]
* [[EcoCyc]]
* [[HumanCyc]]
* [[KEGG]]
* [[PlantCyc]]
* [[Reactome]]
 
* [[Biochemical pathway]]
== See Also ==
* [[Metabolic network]]
* [[Enzyme]]
* [[Gene]]
* [[Biochemistry]]
* [[Molecular biology]]
* [[Systems biology]]
* [[Systems biology]]


== References ==
==References==
{{Reflist}}
* Caspi, R., et al. (2018). The MetaCyc database of metabolic pathways and enzymes. ''Nucleic Acids Research'', 46(D1), D633-D639.
* Karp, P.D., et al. (2019). The BioCyc collection of microbial genomes and metabolic pathways. ''Briefings in Bioinformatics'', 20(4), 1085-1093.


== External Links ==
{{Metabolic Pathways}}
* [MetaCyc Official Website]
{{Biochemistry}}


[[Category:Biological databases]]
[[Category:Biological databases]]
[[Category:Metabolism]]
[[Category:Metabolism]]
[[Category:Bioinformatics]]
[[Category:Bioinformatics]]
{{medicine-stub}}

Latest revision as of 00:49, 9 December 2024

File:Database.png

MetaCyc is a comprehensive metabolic pathway database that provides curated information on metabolic pathways and enzymes from all domains of life. It is a valuable resource for researchers in the fields of biochemistry, molecular biology, and systems biology.

Overview[edit]

MetaCyc is designed to serve as a reference database for metabolic pathways and enzymes. It contains detailed information about individual pathways, including the reactions involved, the enzymes that catalyze these reactions, and the genes that encode these enzymes. MetaCyc is used for a variety of purposes, including the annotation of genomes, the study of metabolic networks, and the development of metabolic models.

History[edit]

MetaCyc was originally developed as part of the EcoCyc project, which focused on the metabolism of Escherichia coli. Over time, MetaCyc expanded to include pathways from a wide range of organisms, making it a universal resource for metabolic pathway information. The database is continuously updated and curated by experts in the field.

Content[edit]

MetaCyc contains information on over 2,500 metabolic pathways, 13,000 reactions, and 11,000 enzymes. The database includes pathways from bacteria, archaea, eukaryotes, and plants. Each pathway entry in MetaCyc provides detailed information, including:

  • A description of the pathway and its biological significance.
  • The list of reactions that comprise the pathway.
  • The enzymes that catalyze each reaction, along with their EC numbers.
  • The genes that encode the enzymes, when known.
  • References to the scientific literature.

Applications[edit]

MetaCyc is used in a variety of research applications, including:

  • Genome Annotation: MetaCyc is used to annotate the metabolic pathways present in newly sequenced genomes.
  • Metabolic Engineering: Researchers use MetaCyc to identify potential targets for metabolic engineering in order to optimize the production of desired compounds.
  • Systems Biology: MetaCyc provides a framework for the construction of metabolic models that can be used to simulate and analyze metabolic networks.

Access and Tools[edit]

MetaCyc is freely accessible online and provides a variety of tools for users, including:

  • Pathway Tools Software: A suite of software tools for pathway analysis and visualization.
  • BioCyc Database Collection: A collection of organism-specific databases that are derived from MetaCyc.
  • Web Services: APIs that allow programmatic access to MetaCyc data.

Also see[edit]

References[edit]

  • Caspi, R., et al. (2018). The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Research, 46(D1), D633-D639.
  • Karp, P.D., et al. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in Bioinformatics, 20(4), 1085-1093.

Template:Metabolic Pathways



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