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 : udpLa4fn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b1241 b0351 b3831 b3752 b4152 b2297 b2458 b2781 b3617 b1612 b1611 b4122 b0907 b1779 b1759 b4161 b4138 b4123 b0621 b4381 b2406 b0452 b3029 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.602783 (mmol/gDw/h)
  Minimum Production Rate : 0.318260 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.657884
  EX_o2_e : 277.359333
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.683194
  EX_pi_e : 1.217968
  EX_so4_e : 0.151793
  EX_k_e : 0.117659
  EX_mg2_e : 0.005229
  EX_ca2_e : 0.003137
  EX_cl_e : 0.003137
  EX_cu2_e : 0.000427
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990319
  EX_h2o_e : 548.121944
  EX_co2_e : 27.533493
  EX_succ_e : 0.628578
  Auxiliary production reaction : 0.318260
  EX_ura_e : 0.109203
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000134

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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