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 (66 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b3553 b1478 b0474 b2518 b1241 b0351 b4069 b3115 b1849 b2296 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b0477 b4139 b1033 b1602 b0507 b3915 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 : 0.459610 (mmol/gDw/h)
  Minimum Production Rate : 0.312676 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.522942
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.963747
  EX_pi_e : 0.443342
  EX_so4_e : 0.115739
  EX_k_e : 0.089713
  EX_fe3_e : 0.007382
  EX_mg2_e : 0.003987
  EX_ca2_e : 0.002392
  EX_cl_e : 0.002392
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.795276
  EX_co2_e : 39.661942
  EX_h_e : 4.498039
  Auxiliary production reaction : 0.312676
  EX_ac_e : 0.267578
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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