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

Gene deletion strategy (71 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b0910 b4152 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b2407 b1612 b1611 b4122 b2690 b3616 b3589 b4374 b0675 b2361 b2291 b3945 b4138 b4123 b0621 b0114 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572371 (mmol/gDw/h)
  Minimum Production Rate : 0.032287 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.017169
  EX_o2_e : 274.694941
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.993350
  EX_pi_e : 0.552113
  EX_so4_e : 0.144134
  EX_k_e : 0.111723
  EX_mg2_e : 0.004965
  EX_cl_e : 0.002979
  EX_ca2_e : 0.002979
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990807
  EX_h2o_e : 543.651833
  EX_co2_e : 25.560196
  EX_ac_e : 2.708754
  EX_succ_e : 0.596864
  EX_ura_e : 0.405896
  Auxiliary production reaction : 0.032287
  EX_glyc__R_e : 0.000191
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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