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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1238 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b4381 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b3821 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.590291 (mmol/gDw/h)
  Minimum Production Rate : 0.883584 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.671522
  EX_o2_e : 273.836135
  EX_nh4_e : 10.794605
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.103733
  EX_so4_e : 0.148647
  EX_k_e : 0.115221
  EX_mg2_e : 0.005121
  EX_ca2_e : 0.003072
  EX_cl_e : 0.003072
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000408
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990519
  EX_h2o_e : 551.287010
  EX_co2_e : 22.446455
  EX_ac_e : 2.242824
  Auxiliary production reaction : 0.883584
  EX_hxan_e : 0.000397
  DM_mththf_c : 0.000264
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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