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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1478 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0477 b1033 b0411 b2799 b3945 b1602 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409664 (mmol/gDw/h)
  Minimum Production Rate : 0.362977 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.761148
  EX_o2_e : 285.971285
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.367024
  EX_pi_e : 0.395165
  EX_so4_e : 0.103162
  EX_k_e : 0.079964
  EX_mg2_e : 0.003554
  EX_ca2_e : 0.002132
  EX_cl_e : 0.002132
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993420
  EX_h2o_e : 552.438977
  EX_co2_e : 35.094214
  EX_ac_e : 1.525429
  Auxiliary production reaction : 0.362977
  EX_xan_e : 0.281605
  EX_ade_e : 0.000276
  DM_mththf_c : 0.000184
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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