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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b2297 b2458 b3617 b1004 b3713 b1109 b0046 b3236 b0261 b3945 b1602 b4381 b3915 b0755 b3612 b2492 b0904 b1380 b2660 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.472261 (mmol/gDw/h)
  Minimum Production Rate : 0.744000 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.880929
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.100378
  EX_pi_e : 0.455546
  EX_so4_e : 0.118925
  EX_k_e : 0.092182
  EX_fe3_e : 0.007585
  EX_mg2_e : 0.004097
  EX_ca2_e : 0.002458
  EX_cl_e : 0.002458
  EX_cu2_e : 0.000335
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.729953
  EX_co2_e : 36.262640
  EX_h_e : 5.407516
  EX_ac_e : 1.060609
  Auxiliary production reaction : 0.744000
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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