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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2242 b3553 b4382 b0474 b2518 b3831 b4384 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4161 b1415 b4138 b4123 b0621 b2406 b3028 b3821 b3918 b0789 b1249 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.565584 (mmol/gDw/h)
  Minimum Production Rate : 0.048094 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.656544
  EX_o2_e : 279.941333
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.807476
  EX_pi_e : 0.545566
  EX_so4_e : 0.142425
  EX_k_e : 0.110398
  EX_mg2_e : 0.004906
  EX_ca2_e : 0.002944
  EX_cl_e : 0.002944
  EX_cu2_e : 0.000401
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.939440
  EX_h2o_e : 548.975045
  EX_co2_e : 30.966604
  EX_succ_e : 0.589787
  EX_ura_e : 0.246653
  Auxiliary production reaction : 0.048094
  EX_pheme_e : 0.003383
  EX_for_e : 0.001387
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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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