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

Model : iML1515 [2].
Target metabolite : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b0411 b0822 b2868 b1727 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390350 (mmol/gDw/h)
  Minimum Production Rate : 0.248375 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 40.950235
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.713812
  EX_pi_e : 0.624910
  EX_so4_e : 0.098298
  EX_k_e : 0.076194
  EX_fe2_e : 0.006269
  EX_mg2_e : 0.003386
  EX_ca2_e : 0.002032
  EX_cl_e : 0.002032
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 53.086789
  EX_co2_e : 41.534218
  EX_h_e : 4.312013
  Auxiliary production reaction : 0.248375
  EX_ac_e : 0.227256
  EX_ade_e : 0.000263
  EX_mththf_e : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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: 21-Sep-2023
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