MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iNJ661 [2].
Target metabolite : cit_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 56: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 7
  Gene deletion: Rv3319 Rv0247c Rv0248c Rv1240 Rv1188 Rv0694 Rv1311   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.043178 (mmol/gDw/h)
  Minimum Production Rate : 0.429069 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glyc_e : 1.000000
  EX_glc__D_e : 1.000000
  EX_o2_e : 1.000000
  EX_nh4_e : 0.814957
  EX_pi_e : 0.047853
  EX_glu__L_e : 0.019355
  EX_so4_e : 0.002785
  EX_fe3_e : 0.000065

Product: (mmol/gDw/h)
  EX_h_e : 2.672192
  EX_h2o_e : 2.413243
  EX_h2_e : 0.942530
  EX_h2co3_e : 0.855937
  Auxiliary production reaction : 0.618005
  EX_val__L_e : 0.552077
  EX_ppa_e : 0.006100

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, .IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 27-Sep-2023
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