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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b1033 b0261 b0411 b2799 b1602 b0507 b4381 b3915 b0452 b0755 b3612 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b2660 b1771 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.341413 (mmol/gDw/h)
  Minimum Production Rate : 0.462419 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.147947
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.926065
  EX_pi_e : 1.716583
  EX_so4_e : 0.085975
  EX_k_e : 0.066641
  EX_fe3_e : 0.005485
  EX_mg2_e : 0.002962
  EX_ca2_e : 0.001777
  EX_cl_e : 0.001777
  EX_cu2_e : 0.000242
  EX_mn2_e : 0.000236
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 53.236481
  EX_co2_e : 34.046440
  EX_h_e : 4.994104
  EX_acald_e : 1.113342
  Auxiliary production reaction : 0.462418
  EX_ade_e : 0.000382
  DM_5drib_c : 0.000229
  DM_4crsol_c : 0.000076

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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