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 : acald_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b1004 b3713 b1109 b0046 b3236 b1779 b1033 b1602 b2342 b3845 b2913 b3915 b0509 b3125 b1380 b1771 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.603464 (mmol/gDw/h)
  Minimum Production Rate : 0.203966 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.445441
  EX_o2_e : 283.430439
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.517358
  EX_pi_e : 0.582105
  EX_so4_e : 0.151964
  EX_k_e : 0.117792
  EX_mg2_e : 0.005235
  EX_cl_e : 0.003141
  EX_ca2_e : 0.003141
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990308
  EX_h2o_e : 550.753614
  EX_co2_e : 34.822649
  EX_acald_e : 0.203966
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000135

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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