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 : ppa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 5: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b3708 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1033 b0335 b2799 b3945 b1602 b0507 b0153 b0584 b0728 b0529 b3821 b1380 b2660 b0606 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610458 (mmol/gDw/h)
  Minimum Production Rate : 0.027363 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.545004
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.592894
  EX_pi_e : 0.588851
  EX_so4_e : 0.153726
  EX_k_e : 0.119157
  EX_fe2_e : 0.009805
  EX_mg2_e : 0.005296
  EX_ca2_e : 0.003177
  EX_cl_e : 0.003177
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.981923
  EX_co2_e : 34.861416
  EX_h_e : 5.636494
  Auxiliary production reaction : 0.027363
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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