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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b0474 b2518 b2744 b1278 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4374 b4161 b0675 b2361 b2291 b1415 b1602 b4138 b4123 b0621 b3028 b3821 b1380 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.512308 (mmol/gDw/h)
  Minimum Production Rate : 0.033822 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.885440
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.259491
  EX_pi_e : 0.494176
  EX_so4_e : 0.129009
  EX_k_e : 0.099999
  EX_fe2_e : 0.008228
  EX_mg2_e : 0.004444
  EX_ca2_e : 0.002667
  EX_cl_e : 0.002667
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000354
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.009952
  EX_co2_e : 33.724704
  EX_h_e : 6.502360
  EX_succ_e : 0.534231
  EX_ura_e : 0.363302
  Auxiliary production reaction : 0.033822
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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