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 (17 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b3942 b1732 b1241 b0351 b2930 b4232 b3697 b3925 b1004 b3713 b1109 b0046 b3236 b2690 b2463 b2210 b3551 b3945 b1602 b4219 b1832 b1778 b0452 b1727 b1380 b1710 b2480 b1206 b0606 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430823 (mmol/gDw/h)
  Minimum Production Rate : 0.449259 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.217776
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.652856
  EX_pi_e : 0.415575
  EX_so4_e : 0.108490
  EX_k_e : 0.084094
  EX_mg2_e : 0.003737
  EX_fe2_e : 0.003556
  EX_fe3_e : 0.003364
  EX_ca2_e : 0.002242
  EX_cl_e : 0.002242
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 42.513177
  EX_co2_e : 33.634680
  EX_h_e : 5.357003
  EX_etoh_e : 2.945937
  EX_ac_e : 0.496544
  Auxiliary production reaction : 0.449259
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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