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 : uaccg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3916 b1241 b0351 b3831 b4069 b3614 b0910 b3752 b4152 b3115 b1849 b2296 b2781 b1850 b1612 b1611 b4122 b1759 b1200 b3616 b3589 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b1723 b3918 b4042 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536902 (mmol/gDw/h)
  Minimum Production Rate : 0.283562 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.864291
  EX_o2_e : 267.053292
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.843543
  EX_pi_e : 1.085023
  EX_so4_e : 0.135203
  EX_k_e : 0.104800
  EX_mg2_e : 0.004658
  EX_ca2_e : 0.002795
  EX_cl_e : 0.002795
  EX_cu2_e : 0.000381
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991377
  EX_h2o_e : 536.114247
  EX_co2_e : 17.208374
  EX_dha_e : 3.942813
  EX_succ_e : 0.559877
  EX_ac_e : 0.312577
  Auxiliary production reaction : 0.283562
  EX_ura_e : 0.097181
  DM_mththf_c : 0.000241
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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