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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b4269 b0493 b3588 b3003 b3011 b2744 b0871 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b0675 b2361 b0261 b3945 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479261 (mmol/gDw/h)
  Minimum Production Rate : 0.039791 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.705841
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.573881
  EX_pi_e : 0.621461
  EX_so4_e : 0.120687
  EX_k_e : 0.093548
  EX_fe3_e : 0.007697
  EX_mg2_e : 0.004158
  EX_ca2_e : 0.002495
  EX_cl_e : 0.002495
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.258119
  EX_co2_e : 39.531670
  EX_h_e : 4.650080
  Auxiliary production reaction : 0.039791
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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