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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b2242 b3831 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b1415 b4015 b0411 b4138 b4123 b0621 b4381 b3028 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.575725 (mmol/gDw/h)
  Minimum Production Rate : 0.304066 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.497532
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.034331
  EX_pi_e : 0.859414
  EX_so4_e : 0.144979
  EX_k_e : 0.112378
  EX_fe2_e : 0.009247
  EX_mg2_e : 0.004994
  EX_ca2_e : 0.002997
  EX_cl_e : 0.002997
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.266016
  EX_co2_e : 30.508776
  EX_h_e : 7.612742
  EX_succ_e : 0.600362
  Auxiliary production reaction : 0.304066
  EX_ura_e : 0.104208
  EX_for_e : 0.001412
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000128

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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