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

SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA.
Nucleic Acids Research (Impact Factor: 9.11). 11/2011; 40(Database issue):D742-53. DOI: 10.1093/nar/gkr1014
Source: PubMed


The MetaCyc database ( provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30,000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc ( is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.

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    • "pH of the MSM might explain the significant presence of type II methanotrophs in our BF ( Pieja et al . , 2011 ) . L opez et al . ( 2014 ) also found Xanthomonadales - related organisms ( bands 8e10 ) in a bioreactor treating CH 4 . Similarly , bacteria from the order Cau - lobacterales have been also identified as possible degraders of methanol ( Caspi et al . , 2010 ) . Finally , the family Microbacteriaceae ( band 14 ) , belonging to the Actinobacteria phylum , has been previously associated to the biodegradation of CH 4 in a coal - packed BF ( Limbri et al . , 2014 ) . On the other hand , 7 fungal species initially present in the compost , including Graphium sp . , disappeared throughout the oper"
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    • "(B) Schematic representation of transcriptional changes of genes on metabolic pathways from glucose/fructose 6P. Each arrow represents a single reaction; reversibility is indicated by a two-arrow line according to the BioCyc database (Caspi et al., 2010). For a matter of simplicity, only the main metabolites are shown; thus, the reactions are not necessarily balanced. "
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    ABSTRACT: Many mammalian cell lines used in the manufacturing of biopharmaceuticals exhibit high glycolytic flux predominantly channelled to the production of lactate. The accumulation of lactate in culture reduces cell viability and may also decrease product quality. In this work, we engineered a HEK 293 derived cell line producing recombinant gene therapy retroviral vector, by down-regulating hypoxia inducible factor 1 (HIF1) and pyruvate dehydrogenase kinase (PDK). Specific productivity of infectious viral titers could be increased more than 20-fold for single gene knock-down (HIF1 or PDK) and more than 30-fold under combined down-regulation. Lactate production was reduced up to 4-fold. However, the reduction in lactate production, alone, was not sufficient to enhance the titer: high-titer clones also showed significant enrolment of metabolic routes not related to lactate production. Transcriptome analysis indicated activation of biological amines metabolism, detoxification routes, including glutathione metabolism, pentose phosphate pathway, glycogen biosynthesis and amino acid catabolism. The latter were validated by enzyme activity assays and metabolite profiling, respectively. High-titer clones also presented substantially increased transcript levels of the viral genes expression cassettes. The results herein presented demonstrate the impact of HIF1 and PDK down-regulation on the production performance of a mammalian cell line, reporting one of the highest fold-increase in specific productivity of infectious virus titers achieved by metabolic engineering. They additionally highlight the contribution of secondary pathways, beyond those related to lactate production, that can be also explored to pursue improved metabolic status favouring a high-producing phenotype. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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    • "Since publication of MetaPathways (Konwar et al., 2013), a modular annotation and analysis pipeline that enables construction of environmental pathway/genome databases (ePGDBs) using Pathway Tools (Karp et al., 2002b, 2010) and MetaCyc (Karp et al., 2000, 2002a; Caspi et al., 2012), there have been improvements to the software via the Knowledge Engine data structure, a graphical user interface (GUI) for data management and browsing, and a master-worker model for task distribution on grids and clouds (Hanson et al., 2014b). Version 2.5 features faster and more accurate quantitative functional and taxonomic inference. "
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    ABSTRACT: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. While this data deluge has enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated GUI allows for keyword annotation query and projection onto user defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. © The Author(s) 2015. Published by Oxford University Press.
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