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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b0474 b2518 b1241 b4069 b4384 b2297 b2458 b2925 b2097 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b3946 b0825 b1623 b1602 b0507 b2975 b3603 b2492 b0904 b3029 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465700 (mmol/gDw/h)
  Minimum Production Rate : 0.247140 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.476459
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.029522
  EX_pi_e : 0.449217
  EX_so4_e : 0.117273
  EX_k_e : 0.090901
  EX_mg2_e : 0.004040
  EX_fe2_e : 0.003843
  EX_fe3_e : 0.003636
  EX_ca2_e : 0.002424
  EX_cl_e : 0.002424
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.891749
  EX_co2_e : 39.595713
  EX_h_e : 4.553799
  EX_ac_e : 0.271124
  Auxiliary production reaction : 0.249062
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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