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 : pg120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b0474 b2518 b2744 b1278 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b2492 b0904 b2197 b3918 b2240 b1695 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483020 (mmol/gDw/h)
  Minimum Production Rate : 0.070349 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 997.791465
  EX_h_e : 991.353915
  EX_o2_e : 280.129743
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.901644
  EX_pi_e : 0.536273
  EX_so4_e : 0.121634
  EX_k_e : 0.094282
  EX_mg2_e : 0.004190
  EX_ca2_e : 0.002514
  EX_cl_e : 0.002514
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 997.783707
  EX_h2o_e : 546.465945
  EX_co2_e : 32.461808
  EX_succ_e : 0.503690
  EX_hxa_e : 0.369512
  EX_ura_e : 0.342533
  Auxiliary production reaction : 0.070349
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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