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

Model : iMM904 [2].
Target metabolite : dmlz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (160 of 163: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YBR069C YPL061W YNL270C YEL063C YPL148C YAL054C YBR085W YMR056C YBL030C YLR089C YCL025C YKR039W YEL047C YOR120W YLL043W YBR192W YMR189W YGR191W YMR250W YHR208W YJR078W YJL121C YPL188W YJR049C YEL041W YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.182157 (mmol/gDw/h)
  Minimum Production Rate : 0.057939 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.362261
  EX_o2_e : 0.192390
  EX_pi_e : 0.056888
  EX_so4_e : 0.014081

Product: (mmol/gDw/h)
  EX_co2_e : 17.218630
  EX_etoh_e : 16.568377
  EX_h2o_e : 3.412750
  EX_h_e : 1.692307
  EX_2hb_e : 0.316361
  EX_ibutoh_e : 0.184980
  EX_for_e : 0.116820
  EX_gly_e : 0.058884
  Auxiliary production reaction : 0.057939
  EX_pap_e : 0.010438

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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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