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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b2836 b1478 b4382 b3942 b1732 b1241 b0351 b4384 b2744 b3614 b0910 b2781 b3844 b1851 b1004 b3713 b1109 b0046 b1779 b2463 b1759 b2210 b4374 b0675 b3551 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b0590 b0529 b1380 b3918 b1710 b2480 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577668 (mmol/gDw/h)
  Minimum Production Rate : 0.080947 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.500127
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.238760
  EX_pi_e : 0.557222
  EX_so4_e : 0.145468
  EX_k_e : 0.112757
  EX_fe2_e : 0.009278
  EX_mg2_e : 0.005011
  EX_ca2_e : 0.003007
  EX_cl_e : 0.003007
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.987483
  EX_co2_e : 35.651934
  EX_h_e : 5.574294
  EX_3hpp_e : 0.104560
  Auxiliary production reaction : 0.080947
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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