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 (76 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2744 b4152 b2297 b2458 b2926 b3617 b1612 b1611 b4122 b3962 b4267 b1033 b4374 b0675 b4138 b4123 b0621 b4381 b2406 b0114 b0529 b2492 b0904 b0325 b0516 b4266 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363277 (mmol/gDw/h)
  Minimum Production Rate : 0.074047 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.967768
  EX_o2_e : 283.037118
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.841662
  EX_pi_e : 0.350419
  EX_so4_e : 0.091480
  EX_k_e : 0.070909
  EX_mg2_e : 0.003151
  EX_cl_e : 0.001891
  EX_ca2_e : 0.001891
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994165
  EX_h2o_e : 550.095444
  EX_co2_e : 32.817153
  EX_succ_e : 0.779334
  EX_thym_e : 0.645870
  EX_alltn_e : 0.400511
  EX_ac_e : 0.211495
  DM_mththf_c : 0.074210
  Auxiliary production reaction : 0.074047
  EX_ura_e : 0.012259
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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