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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b1241 b0351 b3831 b3708 b3008 b3614 b0910 b4152 b0871 b2779 b0030 b2407 b1238 b1612 b1611 b4122 b0651 b2162 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b4138 b4123 b0621 b4381 b2406 b2868 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b0494 b4141 b1798 b1518 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449688 (mmol/gDw/h)
  Minimum Production Rate : 0.085336 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.222805
  EX_o2_e : 286.192705
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.605177
  EX_pi_e : 0.604416
  EX_so4_e : 0.113241
  EX_k_e : 0.087776
  EX_mg2_e : 0.003901
  EX_ca2_e : 0.002341
  EX_cl_e : 0.002341
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992776
  EX_h2o_e : 551.423269
  EX_co2_e : 36.870181
  EX_succ_e : 0.487397
  EX_ura_e : 0.337362
  Auxiliary production reaction : 0.085322
  EX_hxan_e : 0.018467
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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