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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b2779 b2926 b2781 b1612 b1611 b4122 b2690 b1759 b3945 b4138 b4123 b0621 b4381 b2406 b2197 b3918 b4042 b1695 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.411472 (mmol/gDw/h)
  Minimum Production Rate : 0.216978 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.897412
  EX_o2_e : 278.918905
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.027449
  EX_pi_e : 0.613887
  EX_so4_e : 0.103617
  EX_k_e : 0.080316
  EX_mg2_e : 0.003570
  EX_ca2_e : 0.002142
  EX_cl_e : 0.002142
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993391
  EX_h2o_e : 544.719067
  EX_co2_e : 31.534531
  EX_ac_e : 1.089767
  EX_succ_e : 0.429079
  EX_ura_e : 0.291794
  Auxiliary production reaction : 0.216978
  EX_hxa_e : 0.000677
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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