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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b4382 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2925 b2097 b3617 b2407 b1004 b3713 b1109 b0046 b2690 b1982 b2210 b3945 b1602 b2406 b0114 b0529 b2492 b0904 b1380 b0515 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.374492 (mmol/gDw/h)
  Minimum Production Rate : 1.435909 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.045865
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.353215
  EX_pi_e : 0.361237
  EX_so4_e : 0.094305
  EX_k_e : 0.073098
  EX_fe2_e : 0.006015
  EX_mg2_e : 0.003249
  EX_ca2_e : 0.001949
  EX_cl_e : 0.001949
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 47.350669
  EX_co2_e : 27.408248
  EX_h_e : 9.897493
  EX_ac_e : 2.147527
  Auxiliary production reaction : 1.435909
  EX_alltn_e : 0.000252
  EX_glyclt_e : 0.000251
  DM_mththf_c : 0.000168
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000084

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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