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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b3399 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b0474 b2518 b3831 b2744 b0871 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b2498 b0675 b2361 b2291 b0261 b1602 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b1771 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470449 (mmol/gDw/h)
  Minimum Production Rate : 0.089742 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.952346
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.375141
  EX_pi_e : 0.543541
  EX_so4_e : 0.118469
  EX_k_e : 0.091828
  EX_fe3_e : 0.007556
  EX_mg2_e : 0.004081
  EX_ca2_e : 0.002449
  EX_cl_e : 0.002449
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.799636
  EX_co2_e : 38.099457
  EX_h_e : 5.535344
  EX_ura_e : 0.422808
  Auxiliary production reaction : 0.089742
  EX_glyclt_e : 0.000526
  DM_5drib_c : 0.000316
  DM_4crsol_c : 0.000105

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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