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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b2883 b1779 b1982 b3665 b0675 b2361 b0411 b4388 b4381 b0112 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379288 (mmol/gDw/h)
  Minimum Production Rate : 1.213634 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.600652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.524821
  EX_pi_e : 1.579497
  EX_so4_e : 0.095512
  EX_k_e : 0.074034
  EX_fe2_e : 0.006092
  EX_mg2_e : 0.003290
  EX_ca2_e : 0.001974
  EX_cl_e : 0.001974
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 52.571993
  EX_co2_e : 35.271693
  EX_h_e : 5.913592
  Auxiliary production reaction : 1.213634
  EX_acald_e : 0.938176
  EX_ade_e : 0.000255
  DM_mththf_c : 0.000170
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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