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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b0411 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379473 (mmol/gDw/h)
  Minimum Production Rate : 0.727419 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.522417
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.736393
  EX_pi_e : 1.820880
  EX_so4_e : 0.095559
  EX_k_e : 0.074070
  EX_fe3_e : 0.006095
  EX_mg2_e : 0.003292
  EX_ca2_e : 0.001975
  EX_cl_e : 0.001975
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 53.991089
  EX_co2_e : 34.531897
  EX_h_e : 7.686039
  EX_ac_e : 1.282497
  Auxiliary production reaction : 0.727419
  EX_12ppd__R_e : 0.017339
  EX_hxan_e : 0.000255
  DM_5drib_c : 0.000085
  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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