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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b4467 b2836 b1478 b4382 b0474 b2518 b1241 b3831 b4069 b4384 b2297 b2458 b2781 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b0651 b2162 b1759 b1982 b4139 b1623 b4161 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b2223 b2406 b3915 b2975 b3603 b1297 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b3918 b4042 b3662 b1985 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366054 (mmol/gDw/h)
  Minimum Production Rate : 0.688895 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.087785
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.399467
  EX_pi_e : 0.353098
  EX_so4_e : 0.092180
  EX_k_e : 0.071451
  EX_fe3_e : 0.005879
  EX_mg2_e : 0.003176
  EX_ca2_e : 0.001905
  EX_cl_e : 0.001905
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 54.703418
  EX_co2_e : 38.147243
  EX_h_e : 7.094812
  Auxiliary production reaction : 0.688895
  EX_ac_e : 0.213112
  EX_3hpp_e : 0.066257
  EX_hxan_e : 0.000410
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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