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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b1855 b1478 b1241 b0351 b3708 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2920 b4015 b2799 b3945 b1602 b2913 b0452 b0728 b0529 b1380 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.571112 (mmol/gDw/h)
  Minimum Production Rate : 0.025600 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.866133
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.347155
  EX_pi_e : 0.602097
  EX_so4_e : 0.143817
  EX_k_e : 0.111477
  EX_fe2_e : 0.009173
  EX_mg2_e : 0.004954
  EX_cl_e : 0.002973
  EX_ca2_e : 0.002973
  EX_cu2_e : 0.000405
  EX_mn2_e : 0.000395
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.614370
  EX_co2_e : 36.020898
  EX_h_e : 5.375600
  Auxiliary production reaction : 0.025600
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000127

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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