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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b1478 b1241 b0351 b2930 b4232 b3697 b3925 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1493 b3517 b4015 b3945 b1602 b1380 b2660 b1695 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545457 (mmol/gDw/h)
  Minimum Production Rate : 1.012436 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.727355
  EX_o2_e : 280.397745
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.890891
  EX_pi_e : 0.526151
  EX_so4_e : 0.137357
  EX_k_e : 0.106469
  EX_mg2_e : 0.004732
  EX_ca2_e : 0.002839
  EX_cl_e : 0.002839
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991239
  EX_h2o_e : 546.469805
  EX_co2_e : 32.070169
  EX_ac_e : 1.252007
  Auxiliary production reaction : 1.012436
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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