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 : fum_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 8: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b2210 b3551 b2799 b3945 b1602 b4138 b4123 b0621 b0153 b2223 b4219 b1832 b1778 b0584 b0529 b1380 b1710 b2480 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.592475 (mmol/gDw/h)
  Minimum Production Rate : 0.208377 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.792150
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.398677
  EX_pi_e : 0.571505
  EX_so4_e : 0.149197
  EX_k_e : 0.115647
  EX_fe2_e : 0.009516
  EX_mg2_e : 0.005140
  EX_ca2_e : 0.003084
  EX_cl_e : 0.003084
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000409
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.910500
  EX_co2_e : 34.848127
  EX_h_e : 5.860648
  EX_fum_e : 0.208377
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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