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EcoSal Plus

Domain 10: Bioinformatics and Systems Biology

The EcoCyc Database

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  • Authors: Peter D. Karp1, Daniel Weaver2, Suzanne Paley3, Carol Fulcher4, Aya Kubo5, Anamika Kothari6, Markus Krummenacker7, Pallavi Subhraveti8, Deepika Weerasinghe9, Socorro Gama-Castro10, Araceli M. Huerta11, Luis Muñiz-Rascado12, César Bonavides-Martinez13, Verena Weiss14, Martin Peralta-Gil15, Alberto Santos-Zavaleta16, Imke Schröder17, Amanda Mackie19, Robert Gunsalus20, Julio Collado-Vides22, Ingrid M. Keseler23, and Ian Paulsen24
  • Editor: James Kaper25
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 2: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 3: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 4: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 5: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 6: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 7: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 8: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 9: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 10: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 11: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 12: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 13: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 14: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 15: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 16: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 17: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; 18: UCLA Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; 19: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; 20: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; 21: UCLA Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; 22: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México; 23: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025; 24: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; 25: University of Maryland School of Medicine, Baltimore, MD
  • Received 16 January 2014 Accepted 17 January 2014 Published 21 March 2014
  • Address correspondence to Peter Karp, pkarp@AI.SRI.COM
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  • Abstract:

    EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of . EcoCyc is an electronic reference source for biologists and for biologists who work with related microorganisms. The database includes information pages on each gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on gene essentiality and on nutrient conditions that do or do not support the growth of . The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.

  • Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013

Key Concept Ranking

Transcription Start Site
0.58190554
Gene Expression and Regulation
0.49926174
Escherichia coli
0.32599625
Regulatory RNAs
0.31828088
0.58190554

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Tables

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Table 1

Genes and gene products in EcoCyc

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 2

Gene annotation status in EcoCyc

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 3

Reactions, compounds, and pathways in EcoCyc

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 4

Regulation-related objects and interactions in EcoCyc

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 5

Comparison of experimental aerobic glucose-limited chemostat growth data with EcoCyc and iJO1366 FBA model predictions (389 reactions active in EcoCyc)

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 6

EcoCyc FBA model performance for aerobic glycerol-limited growth (385 reactions active in EcoCyc)

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 7

EcoCyc FBA model performance for anaerobic glucose-limited growth (383 reactions active in EcoCyc)

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013
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Table 8

EcoCyc FBA model performance for anaerobic glycerol-limited growth (374 reactions active)

Citation: Karp, P, Weaver, D, Paley, S, Fulcher, C, Kubo, A, Kothari, A, Krummenacker, M, Subhraveti, P, Weerasinghe, D, Gama-Castro, S, Huerta, A, Muñiz-Rascado, L, Bonavides-Martinez, C, Weiss, V, Peralta-Gil, M, Santos-Zavaleta, A, Schröder, I, Mackie, A, Gunsalus, R, Collado-Vides, J, Keseler, I, Paulsen, I. 2014. The EcoCyc Database, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0009-2013

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