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 : 4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2779 b2926 b2781 b1851 b1612 b1611 b4122 b1759 b4161 b0411 b4138 b4123 b0621 b4381 b0452 b0509 b3125 b0529 b2197 b1380 b3918 b1912 b0508 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.594343 (mmol/gDw/h)
  Minimum Production Rate : 0.074134 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.521020
  EX_o2_e : 278.618154
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.335942
  EX_pi_e : 0.721574
  EX_so4_e : 0.149667
  EX_k_e : 0.116012
  EX_mg2_e : 0.005156
  EX_cl_e : 0.003094
  EX_ca2_e : 0.003094
  EX_cu2_e : 0.000421
  EX_mn2_e : 0.000411
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990454
  EX_h2o_e : 548.214130
  EX_co2_e : 29.260580
  EX_succ_e : 0.619776
  EX_thymd_e : 0.239670
  EX_ura_e : 0.107674
  Auxiliary production reaction : 0.074134
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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