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 : cpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4382 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b4139 b1623 b0261 b3945 b1602 b2406 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.450128 (mmol/gDw/h)
  Minimum Production Rate : 0.207731 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.467062
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.899999
  EX_pi_e : 0.641927
  EX_so4_e : 0.113351
  EX_k_e : 0.087862
  EX_mg2_e : 0.003905
  EX_fe2_e : 0.003715
  EX_fe3_e : 0.003515
  EX_ca2_e : 0.002343
  EX_cl_e : 0.002343
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.183081
  EX_co2_e : 37.334544
  EX_h_e : 5.232452
  EX_12ppd__S_e : 0.529113
  EX_ac_e : 0.262058
  Auxiliary production reaction : 0.207731
  DM_5drib_c : 0.000302
  DM_4crsol_c : 0.000100

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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