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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b1241 b0351 b2502 b2744 b0871 b2779 b2925 b2097 b2781 b0099 b3617 b2883 b0477 b3946 b0825 b4374 b2361 b2291 b2913 b2868 b0114 b0529 b2492 b0904 b2954 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363308 (mmol/gDw/h)
  Minimum Production Rate : 0.292942 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.239990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.923694
  EX_pi_e : 0.936332
  EX_so4_e : 0.091488
  EX_k_e : 0.070915
  EX_fe2_e : 0.005835
  EX_mg2_e : 0.003152
  EX_ca2_e : 0.001891
  EX_cl_e : 0.001891
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 44.068119
  EX_co2_e : 29.021016
  EX_h_e : 7.912662
  EX_pyr_e : 4.867265
  Auxiliary production reaction : 0.292942
  EX_glyc__R_e : 0.000122
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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