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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4069 b3926 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1779 b0937 b1033 b3945 b1602 b4381 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.433022 (mmol/gDw/h)
  Minimum Production Rate : 0.601157 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.993508
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.676602
  EX_pi_e : 1.018853
  EX_so4_e : 0.109044
  EX_k_e : 0.084523
  EX_mg2_e : 0.003756
  EX_fe2_e : 0.003574
  EX_fe3_e : 0.003381
  EX_ca2_e : 0.002254
  EX_cl_e : 0.002254
  EX_cu2_e : 0.000307
  EX_mn2_e : 0.000299
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.704947
  EX_co2_e : 35.767458
  EX_h_e : 5.517968
  Auxiliary production reaction : 0.601157
  EX_fum_e : 0.451552
  EX_3hpp_e : 0.380603
  EX_ac_e : 0.252099
  DM_mththf_c : 0.000194
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000097

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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