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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b4382 b0238 b0125 b0474 b1241 b0351 b4069 b4384 b3926 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0477 b1602 b0153 b0590 b0529 b1539 b2492 b0904 b1380 b2660 b1771 b1517 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.474566 (mmol/gDw/h)
  Minimum Production Rate : 1.076470 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.355593
  EX_o2_e : 283.932628
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.125269
  EX_pi_e : 0.457769
  EX_so4_e : 0.119505
  EX_k_e : 0.092632
  EX_mg2_e : 0.004117
  EX_cl_e : 0.002470
  EX_ca2_e : 0.002470
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992378
  EX_h2o_e : 546.937188
  EX_co2_e : 35.903072
  EX_glyc_e : 1.076470
  EX_etoh_e : 0.417571
  EX_ac_e : 0.276286
  DM_mththf_c : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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