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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3553 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b1033 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b3915 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447708 (mmol/gDw/h)
  Minimum Production Rate : 0.334878 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.631194
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.176725
  EX_pi_e : 0.766740
  EX_so4_e : 0.112742
  EX_k_e : 0.087389
  EX_fe3_e : 0.007191
  EX_mg2_e : 0.003884
  EX_ca2_e : 0.002330
  EX_cl_e : 0.002330
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.922487
  EX_co2_e : 37.750061
  EX_h_e : 5.723077
  Auxiliary production reaction : 0.334878
  EX_ac_e : 0.260649
  EX_hxan_e : 0.000501
  DM_5drib_c : 0.000300
  DM_4crsol_c : 0.000100

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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