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 : ade_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (132 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b0474 b2518 b1241 b4069 b2502 b2744 b0512 b3115 b1849 b2296 b2925 b2097 b2781 b0099 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b4139 b4374 b2361 b2291 b3945 b1602 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399730 (mmol/gDw/h)
  Minimum Production Rate : 0.295396 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.042528
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.794029
  EX_pi_e : 0.385582
  EX_so4_e : 0.100660
  EX_k_e : 0.078024
  EX_fe2_e : 0.006420
  EX_mg2_e : 0.003468
  EX_ca2_e : 0.002081
  EX_cl_e : 0.002081
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 45.666792
  EX_co2_e : 32.157070
  EX_h_e : 10.129295
  EX_ac_e : 4.979437
  EX_ade_e : 0.295396
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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