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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b4467 b3942 b1732 b0474 b2518 b4069 b4384 b3708 b3752 b3926 b3115 b1849 b2296 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2463 b2797 b3117 b1814 b4471 b2210 b2440 b3551 b1602 b0153 b4219 b1832 b1778 b4381 b0590 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b1380 b1710 b2480 b0494 b1771 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447778 (mmol/gDw/h)
  Minimum Production Rate : 0.189944 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.297272
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.597250
  EX_pi_e : 0.431929
  EX_so4_e : 0.112759
  EX_k_e : 0.087403
  EX_fe2_e : 0.007192
  EX_mg2_e : 0.003884
  EX_ca2_e : 0.002331
  EX_cl_e : 0.002331
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.160002
  EX_co2_e : 36.121487
  EX_h_e : 6.598812
  EX_fum_e : 0.655738
  EX_ac_e : 0.260690
  EX_ins_e : 0.189944
  EX_3hpp_e : 0.150997
  EX_ade_e : 0.000301
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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