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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b3831 b4384 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b2498 b1033 b2799 b3945 b1602 b0507 b2406 b3915 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b2660 b1695 b1518 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493770 (mmol/gDw/h)
  Minimum Production Rate : 0.136760 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.649656
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.881381
  EX_pi_e : 0.476294
  EX_so4_e : 0.124341
  EX_k_e : 0.096381
  EX_fe3_e : 0.007930
  EX_mg2_e : 0.004283
  EX_ca2_e : 0.002570
  EX_cl_e : 0.002570
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.768695
  EX_co2_e : 38.362623
  EX_h_e : 5.093593
  Auxiliary production reaction : 0.136760
  EX_ade_e : 0.000332
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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