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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b1241 b0351 b3708 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2920 b4015 b2799 b3945 b1602 b0153 b0728 b0529 b3035 b3821 b1380 b3623 b2660 b1695 b3546 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588409 (mmol/gDw/h)
  Minimum Production Rate : 0.026375 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.104887
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.539395
  EX_pi_e : 0.620333
  EX_so4_e : 0.148173
  EX_k_e : 0.114853
  EX_fe2_e : 0.009450
  EX_mg2_e : 0.005104
  EX_ca2_e : 0.003063
  EX_cl_e : 0.003063
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 51.334014
  EX_co2_e : 35.294627
  EX_h_e : 5.538414
  Auxiliary production reaction : 0.026375
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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