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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3942 b1732 b0474 b2518 b1241 b0351 b4069 b4384 b1479 b3752 b2297 b2458 b2926 b3617 b2407 b3844 b3236 b2463 b2210 b3665 b3551 b0261 b0411 b4219 b1832 b1778 b4381 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.351015 (mmol/gDw/h)
  Minimum Production Rate : 0.672868 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.310093
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.483584
  EX_pi_e : 0.338591
  EX_so4_e : 0.088393
  EX_k_e : 0.068516
  EX_fe2_e : 0.005638
  EX_mg2_e : 0.003045
  EX_ca2_e : 0.001827
  EX_cl_e : 0.001827
  EX_cu2_e : 0.000249
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 49.376780
  EX_co2_e : 32.338401
  EX_h_e : 9.180011
  EX_ac_e : 1.186084
  EX_mal__L_e : 1.038005
  Auxiliary production reaction : 0.672868
  EX_ade_e : 0.000236
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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