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 : ps180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1855 b2836 b2242 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b0675 b2361 b2291 b1415 b4138 b4123 b0621 b2492 b0904 b2197 b3028 b3918 b1912 b1206 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445093 (mmol/gDw/h)
  Minimum Production Rate : 0.235073 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.343613
  EX_o2_e : 274.731539
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.673308
  EX_pi_e : 0.664412
  EX_so4_e : 0.112083
  EX_k_e : 0.086879
  EX_mg2_e : 0.003861
  EX_ca2_e : 0.002317
  EX_cl_e : 0.002317
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992851
  EX_h2o_e : 543.471516
  EX_co2_e : 28.738813
  EX_succ_e : 0.464139
  EX_ura_e : 0.315636
  Auxiliary production reaction : 0.235073
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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.

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Last updated: 21-Sep-2023
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