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 : pgp120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 91: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b0474 b2518 b3831 b1278 b3752 b4152 b2779 b2781 b1612 b1611 b4122 b1779 b1759 b4161 b4138 b4123 b0621 b4381 b2239 b2406 b3453 b2197 b3918 b0418 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414829 (mmol/gDw/h)
  Minimum Production Rate : 0.007387 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.265359
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.280173
  EX_pi_e : 0.626624
  EX_so4_e : 0.104462
  EX_k_e : 0.080972
  EX_fe2_e : 0.006663
  EX_mg2_e : 0.003599
  EX_ca2_e : 0.002159
  EX_cl_e : 0.002159
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.877832
  EX_co2_e : 38.786020
  EX_h_e : 5.046038
  EX_succ_e : 0.432581
  EX_ura_e : 0.294175
  EX_g3pe_e : 0.211703
  Auxiliary production reaction : 0.007387
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000093

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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