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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b3665 b0411 b2799 b3945 b1602 b3654 b3714 b3664 b0529 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354187 (mmol/gDw/h)
  Minimum Production Rate : 1.115061 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.712925
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.170372
  EX_pi_e : 1.456712
  EX_so4_e : 0.089191
  EX_k_e : 0.069135
  EX_fe2_e : 0.005689
  EX_mg2_e : 0.003073
  EX_ca2_e : 0.001844
  EX_cl_e : 0.001844
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 50.920610
  EX_co2_e : 33.762086
  EX_h_e : 7.989038
  EX_glyclt_e : 1.183241
  Auxiliary production reaction : 1.115061
  EX_ac_e : 0.206203
  DM_mththf_c : 0.000159
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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.

Last updated: 21-Sep-2023
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