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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b3399 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b4384 b2744 b1479 b0871 b2925 b2097 b3617 b0160 b2407 b3236 b0907 b1779 b2463 b3962 b1982 b3946 b2210 b0825 b4267 b3665 b0675 b2361 b1415 b3551 b1014 b0822 b4219 b1832 b1778 b0112 b0114 b0529 b1539 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b1518 b1813 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.263990 (mmol/gDw/h)
  Minimum Production Rate : 0.349243 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.665365
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.998272
  EX_pi_e : 0.953132
  EX_so4_e : 0.066478
  EX_k_e : 0.051529
  EX_mg2_e : 0.002290
  EX_fe2_e : 0.002179
  EX_fe3_e : 0.002061
  EX_ca2_e : 0.001374
  EX_cl_e : 0.001374
  EX_cu2_e : 0.000187
  EX_mn2_e : 0.000182
  EX_zn2_e : 0.000090
  EX_ni2_e : 0.000085

Product: (mmol/gDw/h)
  EX_h2o_e : 43.601215
  EX_co2_e : 26.097701
  EX_h_e : 8.718462
  EX_pyr_e : 4.841921
  EX_acald_e : 1.075399
  Auxiliary production reaction : 0.349243
  EX_ade_e : 0.080197
  EX_mththf_e : 0.080137
  EX_dxylnt_e : 0.000118
  DM_5drib_c : 0.000059
  DM_4crsol_c : 0.000059

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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