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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b3709 b0153 b2913 b0590 b3161 b0112 b2789 b3127 b0452 b2975 b3603 b1539 b2492 b0904 b1533 b3927 b1380 b2965 b0693 b1473 b0514 b4141 b1798 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277149 (mmol/gDw/h)
  Minimum Production Rate : 0.463260 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.395334
  EX_o2_e : 282.660878
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.237557
  EX_pi_e : 1.657119
  EX_so4_e : 0.533052
  EX_k_e : 0.054098
  EX_mg2_e : 0.002404
  EX_ca2_e : 0.001443
  EX_cl_e : 0.001443
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000192
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995549
  EX_h2o_e : 550.764056
  EX_co2_e : 33.715980
  EX_ac_e : 1.662327
  Auxiliary production reaction : 0.463260
  EX_ade_e : 0.000310
  DM_5drib_c : 0.000186
  DM_4crsol_c : 0.000062

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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