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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b4384 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0477 b4139 b3665 b4015 b1602 b3915 b0452 b2492 b0904 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503163 (mmol/gDw/h)
  Minimum Production Rate : 0.164739 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.000514
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.434122
  EX_pi_e : 0.485354
  EX_so4_e : 0.126707
  EX_k_e : 0.098214
  EX_fe3_e : 0.008081
  EX_mg2_e : 0.004365
  EX_cl_e : 0.002619
  EX_ca2_e : 0.002619
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.359409
  EX_co2_e : 38.247618
  EX_h_e : 4.924282
  EX_ac_e : 0.292935
  EX_12ppd__R_e : 0.171322
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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