The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Caspi, Ron ^a   Altman, Tomer ^a   Dreher, Kate ^b   Fulcher, Carol A ^a   Subhraveti, Pallavi ^a   Keseler, Ingrid M ^a   Kothari, Anamika ^a   Krummenacker, Markus ^a   Latendresse, Mario ^a   Mueller, Lukas A ^c   Ong, Quang ^a   Paley, Suzanne ^a   Pujar, Anuradha ^c   Shearer, Alexander G ^a   Travers, Michael ^a   Weerasinghe, Deepika ^a   Zhang, Peifen ^b   Karp, Peter D ^a  

^a SRI INTERNATIONAL   (United States)

^b GEOPHYSICAL LABORATORY   (United States)

^c United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ARTICLE; BIOCYC DATABASE; COMPARATIVE STUDY; COMPUTER INTERFACE; DATA ANALYSIS SOFTWARE; DATA PROCESSING; DNA INTEGRATION; ENZYME ANALYSIS; GENE TRANSFER; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC MODEL; HUMAN; METABOLISM; METABOLITE; METACYC DATABASE; NONHUMAN; ONLINE SYSTEM; OPERON; PATHWAY GENOME DATABASE; PRIORITY JOURNAL; REFERENCE DATABASE;

DATABASES, FACTUAL; ENERGY METABOLISM; ENZYMES; GENOME; GENOMICS; INTERNET; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; SOFTWARE;

EID: 84860490976     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1014     Document Type: Article

References (42)

1. Caspi,R., Altman,T., Dale,J.M., Dreher,K., Fulcher,C.A., Gilham,F., Kaipa,P., Karthikeyan,A.S., Kothari,A., Krummenacker,M. et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 38, D473-D479.
2. Karp,P.D., Paley,S.M., Krummenacker,M., Latendresse,M., Dale,J.M., Lee,T.J., Kaipa,P., Gilham,F., Spaulding,A., Popescu,L. et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform., 11, 40-79.
3. Dale,J.M., Popescu,L. and Karp,P.D. (2010) Machine learning methods for metabolic pathway prediction. BMC Bioinformatics, 11, 15.
4. Karp,P.D. and Caspi,R. (2011) A survey of metabolic databases emphasizing the MetaCyc family. Arch. Toxicol., 85, 1015-1033.
5. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32, D311-D314. (Pubitemid 38081665)
6. Mueller,L.A., Zhang,P. and Rhee,S.Y. (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol., 132, 453-460. (Pubitemid 36715048)
7. Liang,C., Jaiswal,P., Hebbard,C., Avraham,S., Buckler,E.S., Casstevens,T., Hurwitz,B., McCouch,S., Ni,J., Pujar,A. et al. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res., 36, D947-D953. (Pubitemid 351149850)
8. Evsikov,A.V., Dolan,M.E., Genrich,M.P., Patek,E. and Bult,C.J. (2009) MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol., 10, R84.
9. Seo,S. and Lewin,H.A. (2009) Reconstruction of metabolic pathways for the cattle genome. BMC Syst. Biol., 3, 33.
10. Urbanczyk-Wochniak,E. and Sumner,L.W. (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics, 23, 1418-1423. (Pubitemid 47050525)
11. Zhang,P., Dreher,K., Karthikeyan,A., Chi,A., Pujar,A., Caspi,R., Karp,P., Kirkup,V., Latendresse,M., Lee,C. et al. (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol., 153, 1479-1491.
12. Fey,P., Gaudet,P., Curk,T., Zupan,B., Just,E.M., Basu,S., Merchant,S.N., Bushmanova,Y.A., Shaulsky,G., Kibbe,W.A. et al. (2009) dictyBase - a Dictyostelium bioinformatics resource update. Nucleic Acids Res., 37, D515-D519.
13. Doyle,M.A., MacRae,J.I., De Souza,D.P., Saunders,E.C., McConville,M.J. and Likic,V.A. (2009) LeishCyc: a biochemical pathways database for Leishmania major. BMC Syst. Biol., 3, 57.
14. May,P., Christian,J.O., Kempa,S. and Walther,D. (2009) ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics, 10, 209.
15. Bombarely,A., Menda,N., Tecle,I.Y., Buels,R.M., Strickler,S., Fischer-York,T., Pujar,A., Leto,J., Gosselin,J. and Mueller,L.A. (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res., 39, D1149-D1155.
16. Snyder,E.E., Kampanya,N., Lu,J., Nordberg,E.K., Karur,H.R., Shukla,M., Soneja,J., Tian,Y., Xue,T., Yoo,H. et al. (2007) PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res., 35, D401-D406. (Pubitemid 46056240)
17. Cibis,E., Ryznar-Luty,A., Krzywonos,M., Lutoslawski,K. and Miskiewicz,T. (2011) Betaine removal during thermo- and mesophilic aerobic batch biodegradation of beet molasses vinasse: influence of temperature and pH on the progress and efficiency of the process. J. Environ. Manage., 92, 1733-1739.
18. Scaria,J., Janvilisri,T., Fubini,S., Gleed,R.D., McDonough,S.P. and Chang,Y.F. (2011) Clostridium difficile transcriptome analysis using pig ligated loop model reveals modulation of pathways not modulated in vitro. J. Infect. Dis., 203, 1613-1620.
19. Brown,S.D., Guss,A.M., Karpinets,T.V., Parks,J.M., Smolin,N., Yang,S., Land,M.L., Klingeman,D.M., Bhandiwad,A., Rodriguez,M. Jr et al. (2011) Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc. Natl Acad. Sci. U.S.A., 108, 13752-13757.
20. Ruiz,J.C., D'Afonseca,V., Silva,A., Ali,A., Pinto,A.C., Santos,A.R., Rocha,A.A., Lopes,D.O., Dorella,F.A., Pacheco,L.G. et al. (2011) Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One, 6, e18551.
21. Giannone,R.J., Huber,H., Karpinets,T., Heimerl,T., Kuper,U., Rachel,R., Keller,M., Hettich,R.L. and Podar,M. (2011) Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship. PLoS One, 6, e22942.
22. Banerjee,R., Vats,P., Dahale,S., Kasibhatla,S.M. and Joshi,R. (2011) Comparative genomics of cell envelope components in mycobacteria. PLoS One, 6, e19280.
23. Lamichhane,G., Freundlich,J.S., Ekins,S., Wickramaratne,N., Nolan,S.T. and Bishai,W.R. (2011) Essential metabolites of Mycobacterium tuberculosis and their mimics. MBio, 2, e00301-e00310.
24. Landeta,C., Davalos,A., Cevallos,M.A., Geiger,O., Brom,S. and Romero,D. (2011) Plasmids with a chromosome-like role in rhizobia. J. Bacteriol., 193, 1317-1326.
25. Aggarwal,S., Karimi,I.A. and Lee,D.Y. (2011) Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis. FEMS Microbiol. Lett., 315, 115-121.
26. Holder,J.W., Ulrich,J.C., DeBono,A.C., Godfrey,P.A., Desjardins,C.A., Zucker,J., Zeng,Q., Leach,A.L.B., Ghiviriga,I., Dancel,C. et al. (2011) Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet., 7, e1002219.
27. Baumann,K., Dato,L., Graf,A.B., Frascotti,G., Dragosits,M., Porro,D., Mattanovich,D., Ferrer,P. and Branduardi,P. (2011) The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis. BMC Genomics, 12, 218.
28. Burke,G.R. and Moran,N.A. (2011) Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol. Evol., 3, 195-208.
29. Rodrigues,J.L., Serres,M.H. and Tiedje,J.M. (2011) Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus level. Appl. Environ. Microbiol., 77, 5352-5360.
30. Kim,H.U., Kim,S.Y., Jeong,H., Kim,T.Y., Kim,J.J., Choy,H.E., Yi,K.Y., Rhee,J.H. and Lee,S.Y. (2011) Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol. Syst. Biol., 7, 460.
31. Li,J. and Wang,N. (2011) Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation. PLoS One, 6, e21804.
32. Li,J. and Wang,N. (2011) The wxacO gene of Xanthomonas citri ssp. citri encodes a protein with a role in lipopolysaccharide biosynthesis, biofilm formation, stress tolerance and virulence. Mol. Plant Pathol., 12, 381-396.
33. Jaenicke,S., Ander,C., Bekel,T., Bisdorf,R., Droge,M., Gartemann,K.H., Junemann,S., Kaiser,O., Krause,L., Tille,F. et al. (2011) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One, 6, e14519.
34. Karp,P.D., Paley,S. and Romero,P. (2002) The Pathway Tools software. Bioinformatics, 18(Suppl. 1), S225-S232. (Pubitemid 41185657)
35. McDonald,A.G., Boyce,S. and Tipton,K.F. (2009) ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Res., 37, D593-D597.
36. Sayers,E.W., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
37. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
38. Latendresse,M. and Karp,P.D. (2011) Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics, 12, 176.
39. Tao,H., Bausch,C., Richmond,C., Blattner,F.R. and Conway,T. (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol., 181, 6425-6440. (Pubitemid 29512954)
40. Achterberg,T. (2009) SCIP: solving constraint integer programs. Math. Program. Comput., 1, 1-41.
41. Yeh,I., Hanekamp,T., Tsoka,S., Karp,P.D. and Altman,R.B. (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res., 14, 917-924. (Pubitemid 38660510)
42. Latendresse,M. and Karp,P.D. (2010) An advanced web query interface for biological databases. Database, 2010, baq006.