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 (15 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2690 b2463 b2210 b0675 b3551 b0822 b1602 b4219 b1832 b1778 b1380 b1710 b2480 b1695 b1771 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.526377 (mmol/gDw/h)
  Minimum Production Rate : 0.548902 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.793831
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.684830
  EX_pi_e : 0.507747
  EX_so4_e : 0.132552
  EX_k_e : 0.102745
  EX_mg2_e : 0.004566
  EX_fe2_e : 0.004344
  EX_fe3_e : 0.004110
  EX_ca2_e : 0.002740
  EX_cl_e : 0.002740
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.816271
  EX_co2_e : 32.369256
  EX_h_e : 7.853362
  EX_ac_e : 1.914884
  Auxiliary production reaction : 0.548902
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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