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 (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b1241 b4069 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1033 b0411 b2799 b3945 b1602 b2913 b4381 b3915 b3654 b3714 b3664 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b1380 b0516 b1517 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381193 (mmol/gDw/h)
  Minimum Production Rate : 0.399401 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.272391
  EX_o2_e : 285.705137
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.912663
  EX_pi_e : 1.166503
  EX_so4_e : 0.095992
  EX_k_e : 0.074406
  EX_mg2_e : 0.003307
  EX_ca2_e : 0.001984
  EX_cl_e : 0.001984
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993878
  EX_h2o_e : 553.173459
  EX_co2_e : 35.521639
  Auxiliary production reaction : 0.399401
  EX_ac_e : 0.221925
  DM_mththf_c : 0.000171
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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