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 : cytd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 10: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b2242 b3553 b1478 b1241 b0351 b3831 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b1612 b1611 b4122 b3962 b0337 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b3665 b1415 b1014 b1701 b1805 b2799 b3945 b3709 b4138 b4123 b0621 b2913 b4381 b2406 b3161 b0112 b0114 b2366 b2492 b0904 b1533 b3028 b1380 b1473 b4266 b3662 b2842 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.295075 (mmol/gDw/h)
  Minimum Production Rate : 0.837436 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.057990
  EX_o2_e : 283.458203
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.908510
  EX_pi_e : 0.284631
  EX_so4_e : 0.074306
  EX_k_e : 0.057597
  EX_mg2_e : 0.002560
  EX_cl_e : 0.001536
  EX_ca2_e : 0.001536
  EX_cu2_e : 0.000209
  EX_mn2_e : 0.000204
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995261
  EX_h2o_e : 550.394484
  EX_co2_e : 31.132385
  EX_succ_e : 1.191470
  EX_ac_e : 1.121142
  Auxiliary production reaction : 0.837436
  EX_ade_e : 0.441884
  EX_dxylnt_e : 0.000197
  DM_mththf_c : 0.000132
  DM_5drib_c : 0.000066
  DM_4crsol_c : 0.000066

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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